http://2007.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=500&target=Freestym&year=&month=2007.igem.org - User contributions [en]2021-04-10T18:30:41ZFrom 2007.igem.orgMediaWiki 1.16.5http://2007.igem.org/wiki/index.php/User:FreestymUser:Freestym2009-09-14T23:16:56Z<p>Freestym: /* My name? MARTINA */</p>
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===My name? MARTINA === <br />
<br />
[[Image:Martina.jpg|200px]]<br />
<br />
Hey!<br />
<br />
I’m a student of '''Statistics''' from Spain ('''''Barcelona''''', [http://www.uab.es/estudiants UAB]). I have just finished my degree at [http://www.gla.ac.uk University of Glasgow] and next year I’m going to do a Master by Research in Bioinformatics. My topics of interest are Time Series and Stochastic Modelling. <br />
<br />
But when I’m not at University... I’m a lover and addicted of ''sports'', I like to listen music, to play ''djembes'', to spend time in front of my laptop, and to lie on the sun. <br />
Can I recommend you a film?? -> [[Image:Pi1.jpg]]<br />
<br />
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[[Glasgow/Interviews#Martina Marbà|<font face=georgia color=#3366CC size=4> Read Martina's <br> 59 Second <br> Interview </font>]]</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/InterviewsGlasgow/Interviews2007-10-24T16:59:56Z<p>Freestym: /* Martina Marbà */</p>
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|-<br />
!align=center|[[Image:Uog.jpg]] || [[Glasgow|<font face=georgia color=#3366CC size=4>Back To <br> Glasgow's <br> Main Page</font>]] || [[Glasgow/Meet the team|<font face=georgia color=#3366CC size=4>Back To <br> The Team <br> Page</font>]]<br />
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----<br />
== 59 Second Interviews ==<br />
<br />
=== Toby Friend ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
A but achey and sneezy, but I'll get over it.<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
A number of reasons: to take part in cutting edge research (the money); to improve my knowledge of Genetics (my bank balance); do something constructive (earn some money).<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
see 'How and why...'<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
Deleting Spam from my email account.<br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
AI baby!<br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
hackey-sack in the sun!<br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
AI baby!<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
Reading some books and tidying my neglected London bedroom.<br />
<li><br />
'''Tell us a secret.'''<br><br />
ok, but this is between everyone in the world with internet access and me!...<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
My name is Toby Friend<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
My name is Toby Friend,<br />
I said MY NAME IS TOBY FRIEND,<br />
Actually it's Louis Sanchez Fernando<br />
</ol><br />
<br />
=== Rachael Fulton ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
=== Christine Harkness ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
=== Mai-Britt Jensen ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
=== Karolis Kidykas ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
Fine Thanks!<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
I found a leaflet advertising iGEM competition in one of my lectures. It was very appealing offer. I was very interested in biology while at school but engineering won my sympathies back then. It was an opportunity to go into field I am interested in but has little to do with aerospace just before I graduate and submerge myself into professional life.<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
I always thought about any form of life as of a complex machine which we will be able to control one day. This project proved it to me that I was right. Of course I may not be alive to whiteness it!<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
Airbus? ESA? I love Europe, but if bad luck follows me I will consider Boeing or NASA!<br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
Probably not in Biology! Sorry! I have an engineers blood<br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
I could easily name the scariest one, but its hard to think of any favorite one. There were quite a few of them. <br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
Antigravity Engine! Though I know it is probably impossible, but you said anything.<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
Either one of four: Tennis, Travelling, Working on my project, partying <br />
<li><br />
'''Tell us a secret.'''<br><br />
It will no longer be a secret then.<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
That would be harder then to push a camel through a needle hole.<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
Sorry, times up!<br />
</ol><br />
<br />
=== Martina Marbà ===<br />
#'''How are you today?'''<br> Fine!! Thanks..<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br> Firstly, because one day I chose Glasgow for my next stop of my way.<br> Secondly, because I found amazing to be involved in this new and attractive mixture of science for the study of synthetic biology. <br> <br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br> Wow...!! Lots of things!! First, how to work in a team (fact that usually maths or stats students we don't know what is). But scientificly speaking... lots of things as well! I'm sure that not all the things that I could learn, because in English sometimes it's more difficult to well understand everything, but I'm sure that for me it has been a lot.<br />
#'''Where do you see yourself two years from now?'''<br> Discovering lots of new functions and effects of these molecules from the JUNK GENOME.. ;) Well, not, '''I'M JOKING!!''' But I would like be in this stage...<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br> Should I invest all it in science??? ..well, I would invert it for study: "The New Ways to introduce information and knowledge in our brain (our neurons), in the shortest time", like if we were keeping hardrives in our head or something like that.<br><br />
#'''What has been your favourite iGEM moment so far?'''<br> My favourite was when we began to work in Stochastic Modelling... Or not!! The following night after bowling..Do you remember, guys?? (Chris, Maciej, Toby, Karolis)<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br> It would be... an umbrella for the bike.<br><br />
#'''What are you doing this weekend?'''<br> Maybe I will go to "The Fire Festival" near Aberdeen.. but it isn't sure yet!<br><br />
#'''Tell us a secret.'''<br> I don't know now... but for example that.. Sometimes I am afraid to every day.<br><br />
#'''Describe yourself in five words.'''<br> Curious, Lazy, (moment's)Lover, Enjoyable &.. Energetic. <br><br />
#'''Make up a haiku on the spot.'''<br> "El Pinxo li va dir al Panxo, punxa'm si, pero a la panxa no!!" ;)<br />
<br />
=== Lynsey McLeay ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
<br />
=== Christine Merrick ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
I'm good thanks, how are you?<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
I wanted to get loads of lab experience over the summer and asked Susan Rosser if she would take me on in her lab. She agreed to take me on over the summer and a short time later she informed me about the iGEM competition. I went to a presentation and discovered that this was exactly what I want to do. I think the concept of Synthetic Biology is very exciting and is definately something I want to be involved in while I work towards my degree.<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
A whole lot! I have learned so much on a daily basis that when I think back to the start of the project I can't believe how much I've progressed. Three months ago I had never set foot in a research lab and here I am today! I think that's pretty cool.<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
Hopefully two years from now I will have just finished a work placement as part of my degree in a place much sunnier than Glasgow.<br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
I think that basic molecular genetics should be taught as a foundation of biology in schools the same way that anatomy is. It will be in a hundred years why not make it so today? If that wasn't an option I would use it to solve the world's problems in some way, perhaps expressing drugs for the third world in plants, making biofuels improving the environment. <br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
Well, I really like it when we get results, and I’ve loved learning so much from the people I work with, but the international food night was my favourite. Sitting and laughing with the team from so many different backgrounds was great, especially while eating such good food. Maija’s fissu is awesome.<br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
See Genesis. Only kidding. The wheel, surfing, the colour blue or maybe some way making smoke alarms tell the difference between a real fire and burned toast.<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
Some home improvements, the cinema, and possibly a trip to London to see my brother -he doesn't know it yet.<br />
<li><br />
'''Tell us a secret.'''<br><br />
I have a Girls Aloud song on my iPod, and I quite like it too.<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
You ain’t seen nothing yet.<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
From where I’m sitting<br><br />
I see a computer screen<br><br />
With true reflection<br><br />
</ol><br />
<br />
=== Maija Paakkunainen ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
I'm good, just had strawberries for breakfast so i'm feeling very happy.<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
After my eventful exchange year in Scotland I still wanted more great experiences and decided to ask for summer project possibilities in Glasgow and heard about iGEM from Susan Rosser. The competition sounded challenging but good fun so i decided to apply.<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
I've learned how to work with people from very different backgrounds and also discovered a great deal of new techniques and ways of attack.<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
I've graduated from my university back in Finland and hopefully doing some interesting research with a good group of people. Maybe staying abroad again and learning more things about different cultures and lifestyles. <br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
I'd choose a young, growing Finnish company with a great business plan and determined scientists. Possibly in cancer research because I've always found cancer an interesting and challenging thing to study.<br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
Whenever we get the results we're expecting or when we realise something important which gets us one step forward in our study.<br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
The structure of DNA, an efficient cure for cancer, an endless cup of coffee, or maybe a self chargeable mobile phone? Nokia of course.<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
I'm going to Spain to enjoy some sun before going back to cold cold Finland.<br />
<li><br />
'''Tell us a secret.'''<br><br />
I collect fancy paperbags and I'd get upset if someone would fold or wrinkle them.<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
Happy I came to Glasgow.<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
Haiku, what is it?<br><br />
Is it a weird poem?<br><br />
Or a tasty food?<br><br />
Google please help me,<br><br />
Wikipedia<br><br />
knows it all, always.<br><br />
</ol><br />
<br />
=== Scott Ramsay ===<br />
#'''How are you today?'''<br> Exhausted. We just spent the day clearing out our lab now that the project is almost finished.<br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br> I spoke to a lecturer after class who told me about a summer project we'd get to design ourselves and maybe win some prizes for. I thought it'd be a good opportunity to get to know what life in a lab is like before I start my PhD next year.<br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br> An understanding of how many times experiments go wrong before they go right!<br />
#'''Where do you see yourself two years from now?'''<br> Hopefully still halfway through a PhD.<br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br> Set up a scheme to take laboratory science to schools so students can see how much fun and hands-on it is.<br />
#'''What has been your favourite iGEM moment so far?'''<br> Making friends with the team from Edinburgh, and realising they're having setbacks too.<br />
#'''If you could be the inventor of anything, what would it be?'''<br> Already existing? The radio. Imagine how much money you could have made from all the technologies that rely on some sort of radio transmitters. In the future? I'd co-invent a machine that auto-thaws molecular biology reagents with [[User:L.McLeay|Lynsey]]...<br />
#'''What are you doing this weekend?'''<br> How forward!<br />
#'''Tell us a secret.'''<br> I love cheese and jam sandwiches.<br />
#'''Describe yourself in five words.'''<br> Tall, friendly, self-doubting, caffeine loving.<br />
#'''Make up a haiku on the spot.'''<br> Haiku I must write <br> But inventive I am not <br> This will have to do.<br />
<br />
=== Maciej Trybilo ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
Super Terrific!<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
Oh, I had the opportunity to learn new things every day and meet some brilliant people!<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
<li><br />
'''What are you doing this weekend?'''<br><br />
<li><br />
'''Tell us a secret.'''<br><br />
<li><br />
'''Describe yourself in five words.'''<br><br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
</ol></div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/InterviewsGlasgow/Interviews2007-10-24T16:51:37Z<p>Freestym: /* Martina Marbà */</p>
<hr />
<div>{| valign=top cellpadding=3<br />
|-<br />
!align=center|[[Image:Uog.jpg]] || [[Glasgow|<font face=georgia color=#3366CC size=4>Back To <br> Glasgow's <br> Main Page</font>]] || [[Glasgow/Meet the team|<font face=georgia color=#3366CC size=4>Back To <br> The Team <br> Page</font>]]<br />
|}<br />
----<br />
== 59 Second Interviews ==<br />
<br />
=== Toby Friend ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
A but achey and sneezy, but I'll get over it.<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
A number of reasons: to take part in cutting edge research (the money); to improve my knowledge of Genetics (my bank balance); do something constructive (earn some money).<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
see 'How and why...'<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
Deleting Spam from my email account.<br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
AI baby!<br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
hackey-sack in the sun!<br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
AI baby!<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
Reading some books and tidying my neglected London bedroom.<br />
<li><br />
'''Tell us a secret.'''<br><br />
ok, but this is between everyone in the world with internet access and me!...<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
My name is Toby Friend<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
My name is Toby Friend,<br />
I said MY NAME IS TOBY FRIEND,<br />
Actually it's Louis Sanchez Fernando<br />
</ol><br />
<br />
=== Rachael Fulton ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
=== Christine Harkness ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
=== Mai-Britt Jensen ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
=== Karolis Kidykas ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
Fine Thanks!<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
I found a leaflet advertising iGEM competition in one of my lectures. It was very appealing offer. I was very interested in biology while at school but engineering won my sympathies back then. It was an opportunity to go into field I am interested in but has little to do with aerospace just before I graduate and submerge myself into professional life.<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
I always thought about any form of life as of a complex machine which we will be able to control one day. This project proved it to me that I was right. Of course I may not be alive to whiteness it!<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
Airbus? ESA? I love Europe, but if bad luck follows me I will consider Boeing or NASA!<br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
Probably not in Biology! Sorry! I have an engineers blood<br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
I could easily name the scariest one, but its hard to think of any favorite one. There were quite a few of them. <br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
Antigravity Engine! Though I know it is probably impossible, but you said anything.<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
Either one of four: Tennis, Travelling, Working on my project, partying <br />
<li><br />
'''Tell us a secret.'''<br><br />
It will no longer be a secret then.<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
That would be harder then to push a camel through a needle hole.<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
Sorry, times up!<br />
</ol><br />
<br />
=== Martina Marbà ===<br />
#'''How are you today?'''<br> Fine!! Thanks..<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br> Firstly, because one day I chose Glasgow for my next stop of my way.<br> Secondly, because I found amazing to be involved in this new and attractive mixture of science for the study of synthetic biology. <br> <br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br> Wow...!! Lots of things!! First, how to work in a team (fact that usually maths or stats students we don't know what is). But scientificly speaking... lots of things as well! I'm sure that not all the things that I could learn, because in English sometimes it's more difficult to well understand everything, but I'm sure that for me it has been a lot.<br />
#'''Where do you see yourself two years from now?'''<br> Discovering lots of new functions and effects of these molecules from the JUNK GENOME.. ;) Well, not, '''I'M JOKING!!''' But I would like be in this stage...<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br> Should I invest all it in science??? ..well, I would invert it for study: "The New Ways to introduce information and knowledge in our brain (our neurons), in the shortest time", like if we were keeping hardrives in our head or something like that.<br><br />
#'''What has been your favourite iGEM moment so far?'''<br> My favourite was when we began to work in Stochastic Modelling... Or not!! The following night after bowling..Do you remember, guys?? (Chris, Maciej, Toby, Karolis)<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br> It would be... an umbrella for the bike.<br><br />
#'''What are you doing this weekend?'''<br> Maybe I will go to "The Fire Festival" near Aberdeen.. but it isn't sure yet!<br><br />
#'''Tell us a secret.'''<br> I don't know now... but for example that.. Sometimes I am afraid to every day.<br><br />
#'''Describe yourself in five words.'''<br> CURIOUS, LAZY, (moment's)LOVER , ENJOYABLE, and.. ENERGETIC. <br><br />
#'''Make up a haiku on the spot.'''<br> "El Pinxo li va dir al Panxo, punxa'm si, pero a la panxa no!!" ;)<br />
<br />
=== Lynsey McLeay ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
<br />
=== Christine Merrick ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
I'm good thanks, how are you?<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
I wanted to get loads of lab experience over the summer and asked Susan Rosser if she would take me on in her lab. She agreed to take me on over the summer and a short time later she informed me about the iGEM competition. I went to a presentation and discovered that this was exactly what I want to do. I think the concept of Synthetic Biology is very exciting and is definately something I want to be involved in while I work towards my degree.<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
A whole lot! I have learned so much on a daily basis that when I think back to the start of the project I can't believe how much I've progressed. Three months ago I had never set foot in a research lab and here I am today! I think that's pretty cool.<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
Hopefully two years from now I will have just finished a work placement as part of my degree in a place much sunnier than Glasgow.<br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
I think that basic molecular genetics should be taught as a foundation of biology in schools the same way that anatomy is. It will be in a hundred years why not make it so today? If that wasn't an option I would use it to solve the world's problems in some way, perhaps expressing drugs for the third world in plants, making biofuels improving the environment. <br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
Well, I really like it when we get results, and I’ve loved learning so much from the people I work with, but the international food night was my favourite. Sitting and laughing with the team from so many different backgrounds was great, especially while eating such good food. Maija’s fissu is awesome.<br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
See Genesis. Only kidding. The wheel, surfing, the colour blue or maybe some way making smoke alarms tell the difference between a real fire and burned toast.<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
Some home improvements, the cinema, and possibly a trip to London to see my brother -he doesn't know it yet.<br />
<li><br />
'''Tell us a secret.'''<br><br />
I have a Girls Aloud song on my iPod, and I quite like it too.<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
You ain’t seen nothing yet.<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
From where I’m sitting<br><br />
I see a computer screen<br><br />
With true reflection<br><br />
</ol><br />
<br />
=== Maija Paakkunainen ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
I'm good, just had strawberries for breakfast so i'm feeling very happy.<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
After my eventful exchange year in Scotland I still wanted more great experiences and decided to ask for summer project possibilities in Glasgow and heard about iGEM from Susan Rosser. The competition sounded challenging but good fun so i decided to apply.<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
I've learned how to work with people from very different backgrounds and also discovered a great deal of new techniques and ways of attack.<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
I've graduated from my university back in Finland and hopefully doing some interesting research with a good group of people. Maybe staying abroad again and learning more things about different cultures and lifestyles. <br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
I'd choose a young, growing Finnish company with a great business plan and determined scientists. Possibly in cancer research because I've always found cancer an interesting and challenging thing to study.<br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
Whenever we get the results we're expecting or when we realise something important which gets us one step forward in our study.<br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
The structure of DNA, an efficient cure for cancer, an endless cup of coffee, or maybe a self chargeable mobile phone? Nokia of course.<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
I'm going to Spain to enjoy some sun before going back to cold cold Finland.<br />
<li><br />
'''Tell us a secret.'''<br><br />
I collect fancy paperbags and I'd get upset if someone would fold or wrinkle them.<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
Happy I came to Glasgow.<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
Haiku, what is it?<br><br />
Is it a weird poem?<br><br />
Or a tasty food?<br><br />
Google please help me,<br><br />
Wikipedia<br><br />
knows it all, always.<br><br />
</ol><br />
<br />
=== Scott Ramsay ===<br />
#'''How are you today?'''<br> Exhausted. We just spent the day clearing out our lab now that the project is almost finished.<br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br> I spoke to a lecturer after class who told me about a summer project we'd get to design ourselves and maybe win some prizes for. I thought it'd be a good opportunity to get to know what life in a lab is like before I start my PhD next year.<br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br> An understanding of how many times experiments go wrong before they go right!<br />
#'''Where do you see yourself two years from now?'''<br> Hopefully still halfway through a PhD.<br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br> Set up a scheme to take laboratory science to schools so students can see how much fun and hands-on it is.<br />
#'''What has been your favourite iGEM moment so far?'''<br> Making friends with the team from Edinburgh, and realising they're having setbacks too.<br />
#'''If you could be the inventor of anything, what would it be?'''<br> Already existing? The radio. Imagine how much money you could have made from all the technologies that rely on some sort of radio transmitters. In the future? I'd co-invent a machine that auto-thaws molecular biology reagents with [[User:L.McLeay|Lynsey]]...<br />
#'''What are you doing this weekend?'''<br> How forward!<br />
#'''Tell us a secret.'''<br> I love cheese and jam sandwiches.<br />
#'''Describe yourself in five words.'''<br> Tall, friendly, self-doubting, caffeine loving.<br />
#'''Make up a haiku on the spot.'''<br> Haiku I must write <br> But inventive I am not <br> This will have to do.<br />
<br />
=== Maciej Trybilo ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
Super Terrific!<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
Oh, I had the opportunity to learn new things every day and meet some brilliant people!<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
<li><br />
'''What are you doing this weekend?'''<br><br />
<li><br />
'''Tell us a secret.'''<br><br />
<li><br />
'''Describe yourself in five words.'''<br><br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
</ol></div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/InterviewsGlasgow/Interviews2007-10-24T16:32:34Z<p>Freestym: /* Martina Marbà */</p>
<hr />
<div>{| valign=top cellpadding=3<br />
|-<br />
!align=center|[[Image:Uog.jpg]] || [[Glasgow|<font face=georgia color=#3366CC size=4>Back To <br> Glasgow's <br> Main Page</font>]] || [[Glasgow/Meet the team|<font face=georgia color=#3366CC size=4>Back To <br> The Team <br> Page</font>]]<br />
|}<br />
----<br />
== 59 Second Interviews ==<br />
<br />
=== Toby Friend ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
A but achey and sneezy, but I'll get over it.<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
A number of reasons: to take part in cutting edge research (the money); to improve my knowledge of Genetics (my bank balance); do something constructive (earn some money).<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
see 'How and why...'<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
Deleting Spam from my email account.<br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
AI baby!<br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
hackey-sack in the sun!<br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
AI baby!<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
Reading some books and tidying my neglected London bedroom.<br />
<li><br />
'''Tell us a secret.'''<br><br />
ok, but this is between everyone in the world with internet access and me!...<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
My name is Toby Friend<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
My name is Toby Friend,<br />
I said MY NAME IS TOBY FRIEND,<br />
Actually it's Louis Sanchez Fernando<br />
</ol><br />
<br />
=== Rachael Fulton ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
=== Christine Harkness ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
=== Mai-Britt Jensen ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
=== Karolis Kidykas ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
Fine Thanks!<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
I found a leaflet advertising iGEM competition in one of my lectures. It was very appealing offer. I was very interested in biology while at school but engineering won my sympathies back then. It was an opportunity to go into field I am interested in but has little to do with aerospace just before I graduate and submerge myself into professional life.<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
I always thought about any form of life as of a complex machine which we will be able to control one day. This project proved it to me that I was right. Of course I may not be alive to whiteness it!<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
Airbus? ESA? I love Europe, but if bad luck follows me I will consider Boeing or NASA!<br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
Probably not in Biology! Sorry! I have an engineers blood<br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
I could easily name the scariest one, but its hard to think of any favorite one. There were quite a few of them. <br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
Antigravity Engine! Though I know it is probably impossible, but you said anything.<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
Either one of four: Tennis, Travelling, Working on my project, partying <br />
<li><br />
'''Tell us a secret.'''<br><br />
It will no longer be a secret then.<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
That would be harder then to push a camel through a needle hole.<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
Sorry, times up!<br />
</ol><br />
<br />
=== Martina Marbà ===<br />
#'''How are you today?'''<br> Fine!! Thanks..<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br> Firstly, because one day I chose Glasgow for my next stop of my way.<br> Secondly, because I found amazing to be involved in this new and attractive mixture of science for the study of synthetic biology. <br> <br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br> Wow...!! Lots of things!! First, how to work in a team (fact that usually maths or stats students we don't know what is). But scientificly speaking... lots of things as well! I'm sure that not all the things that I could learn, because in English sometimes it's more difficult to well understand everything, but I'm sure that for me it has been a lot.<br />
#'''Where do you see yourself two years from now?'''<br> Discovering lots of new functions and effects of these molecules from the JUNK GENOME.. ;) Well, not, '''I'M JOKING!!''' But I would like be in this stage...<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br> Should I invest all it in science??? ..well, I would invert it for study: "The New Ways to introduce information and knowledge in our brain (our neurons), in the shortest time", like if we were keeping hardrives in our head or something like that.<br><br />
#'''What has been your favourite iGEM moment so far?'''<br> My favourite was when we began to work in Stochastic Modelling... Or not!! The following night after bowling..Do you remember, guys?? (Chris, Maciej, Toby, Karolis)<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br> It would be... an umbrella for the bike.<br><br />
#'''What are you doing this weekend?'''<br> The Fire Festival near Aberdeen.. but it isn't sure yet!<br><br />
#'''Tell us a secret.'''<br> I don't know now... but for example that.. Sometimes I am afraid to every day.<br><br />
#'''Describe yourself in five words.'''<br> CURIOUS, LAZY, (moment's)LOVER , ENJOYABLE, and.. ENERGETIC. <br><br />
#'''Make up a haiku on the spot.'''<br> "El Pinxo li va dir al Panxo, punxa'm si, pero a la panxa no!!" ;)<br />
<br />
=== Lynsey McLeay ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
<br />
=== Christine Merrick ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
I'm good thanks, how are you?<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
I wanted to get loads of lab experience over the summer and asked Susan Rosser if she would take me on in her lab. She agreed to take me on over the summer and a short time later she informed me about the iGEM competition. I went to a presentation and discovered that this was exactly what I want to do. I think the concept of Synthetic Biology is very exciting and is definately something I want to be involved in while I work towards my degree.<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
A whole lot! I have learned so much on a daily basis that when I think back to the start of the project I can't believe how much I've progressed. Three months ago I had never set foot in a research lab and here I am today! I think that's pretty cool.<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
Hopefully two years from now I will have just finished a work placement as part of my degree in a place much sunnier than Glasgow.<br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
I think that basic molecular genetics should be taught as a foundation of biology in schools the same way that anatomy is. It will be in a hundred years why not make it so today? If that wasn't an option I would use it to solve the world's problems in some way, perhaps expressing drugs for the third world in plants, making biofuels improving the environment. <br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
Well, I really like it when we get results, and I’ve loved learning so much from the people I work with, but the international food night was my favourite. Sitting and laughing with the team from so many different backgrounds was great, especially while eating such good food. Maija’s fissu is awesome.<br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
See Genesis. Only kidding. The wheel, surfing, the colour blue or maybe some way making smoke alarms tell the difference between a real fire and burned toast.<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
Some home improvements, the cinema, and possibly a trip to London to see my brother -he doesn't know it yet.<br />
<li><br />
'''Tell us a secret.'''<br><br />
I have a Girls Aloud song on my iPod, and I quite like it too.<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
You ain’t seen nothing yet.<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
From where I’m sitting<br><br />
I see a computer screen<br><br />
With true reflection<br><br />
</ol><br />
<br />
=== Maija Paakkunainen ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
I'm good, just had strawberries for breakfast so i'm feeling very happy.<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
After my eventful exchange year in Scotland I still wanted more great experiences and decided to ask for summer project possibilities in Glasgow and heard about iGEM from Susan Rosser. The competition sounded challenging but good fun so i decided to apply.<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
I've learned how to work with people from very different backgrounds and also discovered a great deal of new techniques and ways of attack.<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
I've graduated from my university back in Finland and hopefully doing some interesting research with a good group of people. Maybe staying abroad again and learning more things about different cultures and lifestyles. <br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
I'd choose a young, growing Finnish company with a great business plan and determined scientists. Possibly in cancer research because I've always found cancer an interesting and challenging thing to study.<br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
Whenever we get the results we're expecting or when we realise something important which gets us one step forward in our study.<br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
The structure of DNA, an efficient cure for cancer, an endless cup of coffee, or maybe a self chargeable mobile phone? Nokia of course.<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
I'm going to Spain to enjoy some sun before going back to cold cold Finland.<br />
<li><br />
'''Tell us a secret.'''<br><br />
I collect fancy paperbags and I'd get upset if someone would fold or wrinkle them.<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
Happy I came to Glasgow.<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
Haiku, what is it?<br><br />
Is it a weird poem?<br><br />
Or a tasty food?<br><br />
Google please help me,<br><br />
Wikipedia<br><br />
knows it all, always.<br><br />
</ol><br />
<br />
=== Scott Ramsay ===<br />
#'''How are you today?'''<br> Exhausted. We just spent the day clearing out our lab now that the project is almost finished.<br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br> I spoke to a lecturer after class who told me about a summer project we'd get to design ourselves and maybe win some prizes for. I thought it'd be a good opportunity to get to know what life in a lab is like before I start my PhD next year.<br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br> An understanding of how many times experiments go wrong before they go right!<br />
#'''Where do you see yourself two years from now?'''<br> Hopefully still halfway through a PhD.<br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br> Set up a scheme to take laboratory science to schools so students can see how much fun and hands-on it is.<br />
#'''What has been your favourite iGEM moment so far?'''<br> Making friends with the team from Edinburgh, and realising they're having setbacks too.<br />
#'''If you could be the inventor of anything, what would it be?'''<br> Already existing? The radio. Imagine how much money you could have made from all the technologies that rely on some sort of radio transmitters. In the future? I'd co-invent a machine that auto-thaws molecular biology reagents with [[User:L.McLeay|Lynsey]]...<br />
#'''What are you doing this weekend?'''<br> How forward!<br />
#'''Tell us a secret.'''<br> I love cheese and jam sandwiches.<br />
#'''Describe yourself in five words.'''<br> Tall, friendly, self-doubting, caffeine loving.<br />
#'''Make up a haiku on the spot.'''<br> Haiku I must write <br> But inventive I am not <br> This will have to do.<br />
<br />
=== Maciej Trybilo ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
Super Terrific!<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
Oh, I had the opportunity to learn new things every day and meet some brilliant people!<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
<li><br />
'''What are you doing this weekend?'''<br><br />
<li><br />
'''Tell us a secret.'''<br><br />
<li><br />
'''Describe yourself in five words.'''<br><br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
</ol></div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/InterviewsGlasgow/Interviews2007-10-24T12:25:38Z<p>Freestym: /* Martina Marbà */</p>
<hr />
<div>{| valign=top cellpadding=3<br />
|-<br />
!align=center|[[Image:Uog.jpg]] || [[Glasgow|<font face=georgia color=#3366CC size=4>Back To <br> Glasgow's <br> Main Page</font>]] || [[Glasgow/Meet the team|<font face=georgia color=#3366CC size=4>Back To <br> The Team <br> Page</font>]]<br />
|}<br />
----<br />
== 59 Second Interviews ==<br />
<br />
=== Toby Friend ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
A but achey and sneezy, but I'll get over it.<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
A number of reasons: to take part in cutting edge research (the money); to improve my knowledge of Genetics (my bank balance); do something constructive (earn some money).<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
see 'How and why...'<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
Deleting Spam from my email account.<br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
AI baby!<br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
hackey-sack in the sun!<br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
AI baby!<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
Reading some books and tidying my neglected London bedroom.<br />
<li><br />
'''Tell us a secret.'''<br><br />
ok, but this is between everyone in the world with internet access and me!...<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
My name is Toby Friend<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
My name is Toby Friend,<br />
I said MY NAME IS TOBY FRIEND,<br />
Actually it's Louis Sanchez Fernando<br />
</ol><br />
<br />
=== Rachael Fulton ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
=== Christine Harkness ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
=== Mai-Britt Jensen ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
=== Karolis Kidykas ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
Fine Thanks!<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
I found a leaflet advertising iGEM competition in one of my lectures. It was very appealing offer. I was very interested in biology while at school but engineering won my sympathies back then. It was an opportunity to go into field I am interested in but has little to do with aerospace just before I graduate and submerge myself into professional life.<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
I always thought about any form of life as of a complex machine which we will be able to control one day. This project proved it to me that I was right. Of course I may not be alive to whiteness it!<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
Airbus? ESA? I love Europe, but if bad luck follows me I will consider Boeing or NASA!<br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
Probably not in Biology! Sorry! I have an engineers blood<br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
I could easily name the scariest one, but its hard to think of any favorite one. There were quite a few of them. <br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
Antigravity Engine! Though I know it is probably impossible, but you said anything.<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
Either one of four: Tennis, Travelling, Working on my project, partying <br />
<li><br />
'''Tell us a secret.'''<br><br />
It will no longer be a secret then.<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
That would be harder then to push a camel through a needle hole.<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
Sorry, times up!<br />
</ol><br />
<br />
=== Martina Marbà ===<br />
#'''How are you today?'''<br> Fine!! Thanks..<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br> Firstly, because one day I chose Glasgow for my following stop in my way.<br> Secondly, because I found amazing to be involved in this new and atractive mixure of science for the study of synthetic biology. <br> <br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br> Wow...!! Lots of things!! First, how to work in a team (fact that usually maths or stats students we don't know what is). But scientificly speaking... lots of things as well! I'm sure that not all the things that I could learn, because in English sometimes it's more difficult to well understand everything, but I'm sure that for me it has been a lot.<br />
#'''Where do you see yourself two years from now?'''<br> Discovering lots of new functions and effects of these molecules from the JUNK GENOME.. ;) Well, not, '''I'M JOKING!!''' But I would like be in this stage...<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br> Should I invert all it to invest in science??? ..well, I would invert it for study: "New Ways to introduce information and knowledge in our brain (our neurons), in the shortest time", like if we were keeping hardrives in our head or something like that.<br><br />
#'''What has been your favourite iGEM moment so far?'''<br> My favourite was when we begun to work in Stochastics... Or well!! The night out after the bowling..well, OUT or IN (depends..hehhehe)!<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br> It would be an umbrella for the bike.<br><br />
#'''What are you doing this weekend?'''<br> The Fire Festival near Aberdeen.. but it is'nt sure yet!<br><br />
#'''Tell us a secret.'''<br> I don't know... for example.. That sometimes I feel fair of this life?<br><br />
#'''Describe yourself in five words.'''<br> CURIOUS, LAZY, (moment's)LOVER , ENJOYABLE, and.. ENERGETIC. <br><br />
#'''Make up a haiku on the spot.'''<br> "El Pinxo li va dir al Panxo, punxa'm si, pero a la panxa no!!" ;)<br />
<br />
=== Lynsey McLeay ===<br />
#'''How are you today?'''<br><br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
#'''Where do you see yourself two years from now?'''<br><br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
#'''What are you doing this weekend?'''<br><br />
#'''Tell us a secret.'''<br><br />
#'''Describe yourself in five words.'''<br><br />
#'''Make up a haiku on the spot.'''<br><br />
<br />
=== Christine Merrick ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
I'm good thanks, how are you?<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
I wanted to get loads of lab experience over the summer and asked Susan Rosser if she would take me on in her lab. She agreed to take me on over the summer and a short time later she informed me about the iGEM competition. I went to a presentation and discovered that this was exactly what I want to do. I think the concept of Synthetic Biology is very exciting and is definately something I want to be involved in while I work towards my degree.<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
A whole lot! I have learned so much on a daily basis that when I think back to the start of the project I can't believe how much I've progressed. Three months ago I had never set foot in a research lab and here I am today! I think that's pretty cool.<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
Hopefully two years from now I will have just finished a work placement as part of my degree in a place much sunnier than Glasgow.<br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
I think that basic molecular genetics should be taught as a foundation of biology in schools the same way that anatomy is. It will be in a hundred years why not make it so today? If that wasn't an option I would use it to solve the world's problems in some way, perhaps expressing drugs for the third world in plants, making biofuels improving the environment. <br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
Well, I really like it when we get results, and I’ve loved learning so much from the people I work with, but the international food night was my favourite. Sitting and laughing with the team from so many different backgrounds was great, especially while eating such good food. Maija’s fissu is awesome.<br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
See Genesis. Only kidding. The wheel, surfing, the colour blue or maybe some way making smoke alarms tell the difference between a real fire and burned toast.<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
Some home improvements, the cinema, and possibly a trip to London to see my brother -he doesn't know it yet.<br />
<li><br />
'''Tell us a secret.'''<br><br />
I have a Girls Aloud song on my iPod, and I quite like it too.<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
You ain’t seen nothing yet.<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
From where I’m sitting<br><br />
I see a computer screen<br><br />
With true reflection<br><br />
</ol><br />
<br />
=== Maija Paakkunainen ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
I'm good, just had strawberries for breakfast so i'm feeling very happy.<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
After my eventful exchange year in Scotland I still wanted more great experiences and decided to ask for summer project possibilities in Glasgow and heard about iGEM from Susan Rosser. The competition sounded challenging but good fun so i decided to apply.<br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
I've learned how to work with people from very different backgrounds and also discovered a great deal of new techniques and ways of attack.<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
I've graduated from my university back in Finland and hopefully doing some interesting research with a good group of people. Maybe staying abroad again and learning more things about different cultures and lifestyles. <br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
I'd choose a young, growing Finnish company with a great business plan and determined scientists. Possibly in cancer research because I've always found cancer an interesting and challenging thing to study.<br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
Whenever we get the results we're expecting or when we realise something important which gets us one step forward in our study.<br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
The structure of DNA, an efficient cure for cancer, an endless cup of coffee, or maybe a self chargeable mobile phone? Nokia of course.<br />
<li><br />
'''What are you doing this weekend?'''<br><br />
I'm going to Spain to enjoy some sun before going back to cold cold Finland.<br />
<li><br />
'''Tell us a secret.'''<br><br />
I collect fancy paperbags and I'd get upset if someone would fold or wrinkle them.<br />
<li><br />
'''Describe yourself in five words.'''<br><br />
Happy I came to Glasgow.<br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
Haiku, what is it?<br><br />
Is it a weird poem?<br><br />
Or a tasty food?<br><br />
Google please help me,<br><br />
Wikipedia<br><br />
knows it all, always.<br><br />
</ol><br />
<br />
=== Scott Ramsay ===<br />
#'''How are you today?'''<br> Exhausted. We just spent the day clearing out our lab now that the project is almost finished.<br />
#'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br> I spoke to a lecturer after class who told me about a summer project we'd get to design ourselves and maybe win some prizes for. I thought it'd be a good opportunity to get to know what life in a lab is like before I start my PhD next year.<br />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br> An understanding of how many times experiments go wrong before they go right!<br />
#'''Where do you see yourself two years from now?'''<br> Hopefully still halfway through a PhD.<br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br> Set up a scheme to take laboratory science to schools so students can see how much fun and hands-on it is.<br />
#'''What has been your favourite iGEM moment so far?'''<br> Making friends with the team from Edinburgh, and realising they're having setbacks too.<br />
#'''If you could be the inventor of anything, what would it be?'''<br> Already existing? The radio. Imagine how much money you could have made from all the technologies that rely on some sort of radio transmitters. In the future? I'd co-invent a machine that auto-thaws molecular biology reagents with [[User:L.McLeay|Lynsey]]...<br />
#'''What are you doing this weekend?'''<br> How forward!<br />
#'''Tell us a secret.'''<br> I love cheese and jam sandwiches.<br />
#'''Describe yourself in five words.'''<br> Tall, friendly, self-doubting, caffeine loving.<br />
#'''Make up a haiku on the spot.'''<br> Haiku I must write <br> But inventive I am not <br> This will have to do.<br />
<br />
=== Maciej Trybilo ===<br />
<ol><br />
<li><br />
'''How are you today?'''<br><br />
Super Terrific!<br />
<li><br />
'''How and why did you get involved in the University of Glasgow iGEM Team 2007?'''<br><br />
<li><br />
'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
Oh, I had the opportunity to learn new things every day and meet some brilliant people!<br />
<li><br />
'''Where do you see yourself two years from now?'''<br><br />
<li><br />
'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
<li><br />
'''What has been your favourite iGEM moment so far?'''<br><br />
<li><br />
'''If you could be the inventor of anything, what would it be?'''<br><br />
<li><br />
'''What are you doing this weekend?'''<br><br />
<li><br />
'''Tell us a secret.'''<br><br />
<li><br />
'''Describe yourself in five words.'''<br><br />
<li><br />
'''Make up a haiku on the spot.'''<br><br />
</ol></div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/ModelingGlasgow/Modeling2007-10-15T18:18:29Z<p>Freestym: /* Stochastic Modelling */</p>
<hr />
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|}<br />
----<br />
{|cellspacing="6px" cellpadding="16" border="0" width="100%"<br />
|- align=center<br />
|[http://2007.igem.org/Glasgow/Modeling <font face=georgia color=#3366CC size=5><b>Modelling</b></font>]<br />
|[http://2007.igem.org/Glasgow/DryLog <font face=georgia color=#3366CC size=5><b>Log</b></font>]<br />
|[http://2007.igem.org/Glasgow/DryTutorials <font face=georgia color=#3366CC size=5><b>Tutorials</b></font>]<br />
|[http://2007.igem.org/Glasgow/DryReferences <font face=georgia color=#3366CC size=5><b>References</b></font>]<br />
<br />
|}<br />
----<br />
<br />
= Summary =<br />
Synthetic biology has been used to describe an approach to biology<br />
which attempts to design and construct deliberate biological systems<br />
that can be investigated experimentally, which are otherwise very<br />
expensive and practically challenging. One of the central features<br />
of synthetic biology is the appreciation of the knowledge from<br />
science and engineering disciplines for the better design and<br />
understanding of synthetic networks. Here we have engineered a<br />
bacterial biosensor with the involvement of the construction of two<br />
new reporter genes PhzM and PhzS to detect polluting<br />
chemicals, which has the potential to provide an inexpensive and<br />
easy-to-use method of detecting industrial pollution. We explored<br />
a variety of computational approaches to study the behaviour of<br />
three synthetic systems: simple reporter system, positive feedback<br />
reporter system and '''[...]'''. We developed deterministic<br />
and stochastic models that quantitatively describe the graded<br />
signal-response property of the simple reporter system, and also<br />
showed that models can be expanded and used to qualitatively predict<br />
the ''in vivo'' behaviour of the complicated systems. The dynamics<br />
is further studied via the application of qualitative modelling<br />
methods. Simulations reveal that the model with positive feedback<br />
loop has higher output level than that from the intact model '''[...]''' This work shows that by integrating engineering<br />
techniques with scientific methodologies, we can gain a new insights<br />
into the genetic regulation and should become the reference framework<br />
for the design and construction of biochemical networks in synthetic<br />
biology.<br />
<br />
= Framework =<br />
We have used a framework which unifies the qualitative,<br />
stochastic and continuous worlds, as a basis for our overall approach to<br />
modelling<br />
and analysing the biochemical pathways.<br />
Each perspective adds its<br />
contribution to the understanding of the system, thus the three<br />
approaches do not compete, but complement each other. <br />
Qualitative descriptions are abstractions over<br />
stochastic or continuous descriptions, and the stochastic<br />
and continuous models approximate each other. <br />
Note: this framework is based on <br />
David Gilbert, Monika Heiner and Sebastian Lehrack (2007). [[Media:Edinburgh_proceedings.pdf | "A Unifying<br />
Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets"]]. In<br />
proceedings Computational Methods in Systems Biology CMSB 2007 (Computational Methods in Systems Biology),<br />
Springer-Verlag LNCS/LNBI Volume 4695, pp. 200-216.<br />
<br />
Our overall framework is illustrated in<br />
Figure 1 that relates the three major ways of<br />
modelling and analysing biochemical networks that we have used:<br />
qualitative, stochastic and continuous.<br />
<br />
The most abstract representation of a biochemical network is <br />
qualitative and is minimally described by its topology. Initial descriptions<br />
can be obtained from biochemists, and are often in some semiformal<br />
representation. These can easily be transformed into<br />
a formal description at this stage which is usually<br />
a bipartite directed graph with nodes representing biochemical<br />
entities or reactions, or in Petri net terminology places<br />
and transitions '''(link to petrinetsection)'''. <br />
<center>[[Image: FrameworkSlide.png |frame| Figure 1. Conceptual modelling framework]]</center><br />
The qualitative description can be further enhanced by the abstract<br />
representation of discrete quantities of species, achieved in Petri<br />
nets by the use of tokens at places. These can represent the number<br />
of molecules, or the level of concentration, of a species. A<br />
particular arrangement of tokens over a network is called a <br />
marking. The standard semantics for these qualitative Petri<br />
nets (QPN) does not associate a time with transitions or the sojourn<br />
of tokens at places, and thus these descriptions are time-free.<br />
The qualitative analysis considers however all possible behaviour<br />
of the system under any timing. <br />
The behaviour of such a net forms a discrete state<br />
space. <br />
<br />
Timed information can be added to the qualitative description in<br />
two ways -- stochastic and continuous. <br />
The continuous model replaces the discrete values of species with<br />
continuous values, and hence is not able to describe the behaviour<br />
of species at the level of individual molecules, but only the overall<br />
behaviour via concentrations. We can regard the discrete description<br />
of concentration levels as abstracting over the continuous description<br />
of concentrations. Timed information is introduced by the association<br />
of a particular deterministic rate information with each transition,<br />
permitting the continuous model to be represented as a set of<br />
ordinary differential equations (ODEs) '''(link to ODE section)'''. <br />
The concentration of a<br />
particular species in such a model will have the same value at each<br />
point of time for repeated experiments. The state space of such<br />
models is continuous and linear. <br />
It is also possible to linearise ODE descriptions, by for example Laplace transforms, in an attempt to increase modularity in the system description and hence to facilitate model construction ([[Glasgow/Modeling#BioBrick_library |BioBrick library]]). This approach results in transformations from the time-domain, in which inputs and outputs are functions of time, to the frequency-domain.<br />
<br />
The stochastic Petri net (SPN) description preserves the discrete state<br />
description,<br />
but in addition associates a probabilistically distributed firing rate<br />
or rate constant<br />
(waiting time) with each reaction and an associated rate law or hazard<br />
function which depends on the state of the system.<br />
Thus, the time-evolution of a reaction can be regarded as a stochastic<br />
process, and the time-evolution of the states of such a reaction<br />
system can be regarded as a Markov process with a discrete state space.<br />
In this context we can refer to the Chemical Master Equation (CME), which is<br />
equivalent to Kolmorogov's forward equation for a stochastic kinetic process<br />
(Wilkinson, 2006).<br />
It is quite straightforward to simulate such a system, and this is usually<br />
done with the standard discrete event simulation procedure known as "the<br />
Gillespie algorithm" (Gillespie, 1977). <br />
In our project we have directly simulated the system from CMEs using the Gillespie algorithm ([[Glasgow/Modeling#Stochastic_Modelling |Stochastic Modelling]]).<br />
<br />
In summary, the qualitative<br />
time-free description is the most basic, with discrete values<br />
representing numbers of molecules or levels of concentrations.<br />
The qualitative description abstracts over two timed, quantitative models.<br />
In the stochastic description, discrete values for the amounts of species<br />
are retained, but a stochastic rate is associated with each reaction. The continuous model describes amounts of species using continuous values<br />
and associates a deterministic rate with each reaction.<br />
These two time-dependent models can be mutually approximated by hazard<br />
functions belonging to the stochastic world.<br />
The QPN is an abstraction of<br />
the SPN, sharing the same state space and transition relation with<br />
the stochastic model, with the probabilistic information removed.<br />
All qualitative properties valid in the QPN are also valid in the<br />
SPN, and vice versa.<br />
<br />
= Detailed reports =<br />
{| cellspacing="6px" cellpadding="16" border="0" width="100%"<br />
|-<br />
|<br />
== Model Evolution ==<br />
Text<br />
<br />
|<br />
== Stochastic Modelling ==<br />
The stochastic fluctuation in gene expression arises in one of two ways intrinsic and extrinsic noise. Here, intrinsic noise is the focus of interest: Cells<br />
are intrinsically noisy biochemical reactors; low reactant numbers can lead to<br />
significant statistical <br />
fluctuations in molecule numbers and reaction rates.<br />
It has been brought to light that 'gene expression has a stochastic component<br />
due to the single molecule nature of the gene and the small number of copies<br />
of individual DNA-binding proteins in the cell. 'Noise is seen as being<br />
detrimental and volatile in different systems of interest. However, living systems<br />
are inherently noisy and are optimised to function in the presence of<br />
stochastic <br />
fluctuations. In this case the system of interest is a single cell or<br />
bacteria of a bacterial whole cell bio-sensor, noise is investigated on a cellular<br />
level using a stochastic modelling algorithm called Gillespie algorithm. 'A<br />
stochastic model is a tool for estimating probability distributions of potential<br />
outcomes by allowing random variation in one or more inputs over time.It<br />
can give a better prediction of the behaviour of a system, especially on a<br />
single cellular level. It takes into account a number of parameters that contribute<br />
to the model in a random manner rather than assuming everything<br />
can be predicted deterministically. <br><br />
[[Media:GlasgowStochasticModelling.pdf|Full report]]<br />
<br />
|-<br />
|<br />
<br />
== Model Analysis ==<br />
Text<br />
|<br />
== Petri Net Modelling ==<br />
Text<br />
|-<br />
|<br />
== Minicap Sensitivity Analysis Program Package ==<br />
The Multi-Parametric and Initial Concentration Sensitivity analysis [http://compbio.dcs.gla.ac.uk/iGEM2007/Minicap_Sensitivity_Analysis_Program_Package.zip server (Minicap)] package is a Matlab function which executes a chosen Dynamic or Stochastic ''System Function'' for a defined number of different variable values across any desired range. The ''subject'' of analysis can either be constants in the user's system eg. parameters in a biological system (MPSA) or initial values of the variables in the user's system eg. initial substrate concentrations (ISCSA). The program will output a plot for each variable showing a comparison of ''acceptable'' and ''unacceptable'' samples across the subject's range with 3 calculated quantitative comparison figures: the ''Correlation Coefficient'', the ''Area'' between acceptable and unacceptable curves, and the ''Standard Deviation of the gradient'' of the acceptable plot. The comparative and intrinsic sensitivity of each chosen subject is thus highlighted. A plot showing the trend of the ''Substrate of Interest'' over time is also displayed. <br />
<br />
As well as this report, the Minicap package contains a User Manual in html, a number of example codes and all the novel (i.e. not ode15s) function and text files required to run Minicap.<br />
<br />
To see the full PDF report on Minicap [[http://2007.igem.org/wiki/images/f/fb/Minicap.pdf click here]].<br />
<br />
|<br />
<br />
== BioBrick library ==<br />
[[Image:BioBricks.JPG|right|150px]]<br />
[http://compbio.dcs.gla.ac.uk/iGEM2007/BioBricklibrary.zip BioBrickLibrary.zip]<br />
An add on Library to Simulink for modelling dynamical biological systems at Brick (Gene) level. Simulink is a program dedicated for dynamical system simulation, however in depth knowledge of dynamics is needed if one is to simulate system mentioned above. The BioBrick library has all the blocks as well as GUI (Graphical User Interface) needed to do the job without understanding how Simulink works. It uses drag and drop system and shares all constants in Matlab’s .m file, so it is easy to store and update them.<br />
<br />
BioBrick library’s main aim is to tell whether and how different topology will influence the output of the system. If actual rate constants are known it can be used instead or as complimentary to ODE modelling. However it must be noted that ODE rate constants ARE NOT TRANSFERABLE to BioBrick library. <br />
<br />
More information can be found in [[Media:ElectrEcoBluSimulinkManual.pdf|ElectrEcoBluSimulinkManual]] document.<br />
Full [[Media:Report.pdf|Texnical Report (''BioBrick Type Modeling'')]] for concept evolution and justification.<br />
|-<br />
|<br />
<br />
== Microbial Fuel Cell Evaluation ==<br />
[[Image:MFC.jpg|right|150px]]<br />
During the course of the project some introductory work has been done with microbial fuel cells in order to prepare us for the envisaged final stage of the project. We have had three fuel cells at our disposition supplied by the UK's NCBE. The experience we have gained and some of the results have been aggregated in this short work. <br />
|<br />
<br />
|}<br />
----<br />
{|cellspacing="6px" cellpadding="16" border="0" width="100%"<br />
|- align=center<br />
|[http://2007.igem.org/Glasgow/Modeling <font face=georgia color=#3366CC size=5><b>Modelling</b></font>]<br />
|[http://2007.igem.org/Glasgow/DryLog <font face=georgia color=#3366CC size=5><b>Log</b></font>]<br />
|[http://2007.igem.org/Glasgow/DryTutorials <font face=georgia color=#3366CC size=5><b>Tutorials</b></font>]<br />
|[http://2007.igem.org/Glasgow/DryReferences <font face=georgia color=#3366CC size=5><b>References</b></font>]<br />
<br />
|}</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-14T11:33:55Z<p>Freestym: /* 09/08 */</p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We were introduced to the 'Nested Functions' to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menten equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab, explaining the methods we employ, as modellers, to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took us an hour to finalize all the details. And now we have to go again.<br><br />
Lucky for us, modelers, computers dot care much about bacteria used in the experiment so as long as we follow the same pathway, we only need to rename variables. Bless!<br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math's, as Rachel and Kristin does some analytical derivations for our model's optimization. To be honest, we were very optimistic about the outcome, and though, the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack, even for MatLAB. <br><br />
<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done by Maciej.<br><br />
<br />
== Week 3 ==<br />
=== 16/07 ===<br />
Glasgow Bank Holiday.<br />
<br />
=== 17/07 ===<br />
We were given a brief introduction to Bionessie and SBML. Also we be begun to get to grips with Global Sensitivity analysis.<br />
<br />
=== 18/07 ===<br />
A brief overview of SimBiology was given to the drylab by Gary. Martina and Rachel continued learning about Stochastic modelling, while the rest of the team were working on Sensitivity Analysis.<br />
<br />
=== 19/07 ===<br />
A presentation was given to both, the wetlab and the drylab, about the Full Text Fetcher programme which, will help to search and retrive research articles.<br />
The Stochastic Simulation Algorithm (Gillespie's algorithm) is yet ready in the code to run some stochastics simulations on the Michaelis_Menten system.<br />
<br />
=== 20/07 ===<br />
Today we realized that, we missed few important details in our model 1. All morning was like one big mess. Everybody gave their ideas how things should be sorted. <br />
Eventually, we settled our brainstormed ideas on board and decided to leave simulations for Monday because new parameter hunt for model 1.2 was about to begin…<br />
Stochastic's work keeps on fitting the fano factor!<br />
<br />
== Week 4 ==<br />
=== 23/07 ===<br />
Day spent on long discussions with Raya about the accuracy of our model 1.2 . We finally simulated it and… Results were a bit, shall I say, unpleasant. Because of signal degradation, we will not reach a stable state as we anticipated before. That is going to mess up our optimization algorithms, for sure.<br />
<br />
=== 24/07 ===<br />
Kristin was asked by Xu to introduce Petri Net([http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html Snoopy]) method to qualitatively analyse the dynamics of the system. And Karolis, introduced a dynamical approach in modeling of the system using Simulink. Both methods rely not only on blunt programming, but introduce GUI (Graphical User Interface) logics. Respect the Stochastic Model, we have been runing this one by doing some changes in the model (like changes in the signal, or other implementations), and later comparing with the deterministic model the results.<br />
<br />
=== 25/07 ===<br />
Maciek started a thorough research of registry files, because we were told by dry lab, that they are about to deposit their first brick and, it is not very intuitive (a good point for registry’s future development). He promised to study it and give us all tutorial about his findings. We have discussed as well about how we will determinate the parameters for the stochastic model.<br />
<br />
=== 26/07 ===<br />
Bricks. Brick Bricks. What is this brick? What is the aim of having bricks? All these questions were brought forward and we all agreed to do a thorough individual research and combine them in joint brainstorm, because as our grandfathers used to say: ‘There are as many opinions, as there are heads’. Reachel and Martina continue working in cascade models for Stochastics.<br />
<br />
=== 27/07 ===<br />
First bricks from Glasgow team reached a sandpit. No no. Do not rush to copy them. That’s just a ‘getting used to the system’. We are about to deposit real one, so we want everything to go as smooth as possible.<br />
<br />
== Week 5 ==<br />
=== 30/07 ===<br />
Maciek’s tutorial enlightened wet and dry labs about all the registry’s pluses and minuses. We now know how to deposit a brick, edit it and etc. During this tutorial, we compiled a list of ides and suggestions, how to update the concept of brick itself, and some suggestions for registry’s future. Some questions have been asked by Rachael to the weblab to do some changes in the stochastic model.<br />
<br />
=== 31/07 ===<br />
To pursue the further ideas about Brick-Based system modeling Karolis introduced some CAD techniqes for possible GUI algorithm and code development. Rach, beautiful plots about the fano factor!! ;)<br />
<br />
=== 01/08 ===<br />
When the day was about to be over, we received long awaited news… First experimental data have finally reached us. We will be able to do some curve fitting, parameter estimation and other cool stuff?<br />
<br />
=== 02/08 ===<br />
Today we brainstormed the data we have. Everybody added their bit to ideas pot, however, since the data wasn’t that plentiful as we expected, we queried wet-lab for some more input. They promised, that more data is on the way. Stochastics are runing the code for several numbers of cells, and it take long time to run those!<br />
<br />
=== 03/08 ===<br />
Friday. The end of week 5. Our project just passed major milestone. No, not in development, but in time left available for us to complete it. We are, officially, halfway to successes now?<br />
<br />
== Week 6 ==<br />
=== 06/08 ===<br />
Today we received extra data to support our estimations. General modelers meting raised issues like the further development of the model, feedback loops, or our possible influence for wet lab. Now, that we have some data, (input) we should produce some output for near future projects. Stochastics keep on runing simulations of data.<br />
<br />
=== 07/08 ===<br />
Day was full of events. First thing in the morning, we had a modelers meeting, to discuss our final model’s layout. General structure and equations were drafted on board. From now we will be analyzing previous data from lab and try to simulate new model, called Model F1. <br><br />
Edinburgh team came to visit us after lunch. We exchanged some ideas about project, including modeling approaches and wet lab techniques used. After a brief introduction, we decided to continue our conversation outside the lab, so went to check what Glasgow could offer us.<br />
<br />
=== 08/008 ===<br />
Most of the day spent on Model F1, Model F1 Fedback and Model F1 Constitutive. Discussion about the stochastics full model to be able to compared with the deterministic one.<br />
<br />
=== 09/08 ===<br />
Even more types of models have been suggested to simulate. We have so much data now, so in order to manage it, we decided to document everything in LATEX. General standards are agreed for all the constants and equation. These are to be officially published later on. The propensities function reactions have been determinated for our stochastic model, let's go to codify them.<br />
<br />
=== 10/08 ===<br />
Today we realized, that even almighty MATLAB, is not always the best solution. Since our experiments require LHS (Latin Hypercube Sampling) in huge numbers and Matlab does it in one hour. We decided to switch back to Good Old C++. Job well done and in 10 SECONDS ONLY???!!!! What has just happened knows only Maciek himself. Only he knows The Way Of Gods.<br />
<br />
== Week 7 ==<br />
=== 13/08 ===<br />
The day was quite productive, nerveless lucky. We manage to find 3 parameters of our interest. Besides that, we came with idea, how to compare qualitatively models F2 and F3 feedback. The method we developed and called ‘Feedback Logics’ allowed us to optimize four unknowns in F3 feedback. Results that came out suggested that addition of feedback loop for F3 will not influence the outcome of *** (sorry classified). Tomorrows meeting will decide, if F3 is wrong or it is the outcome one could expect.<br />
<br />
=== 14/08 ===<br />
?<br />
=== 15/008 ===<br />
?<br />
=== 16/08 ===<br />
?<br />
=== 17/08 ===<br />
?</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-14T11:30:28Z<p>Freestym: /* 08/008 */</p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We were introduced to the 'Nested Functions' to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menten equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab, explaining the methods we employ, as modellers, to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took us an hour to finalize all the details. And now we have to go again.<br><br />
Lucky for us, modelers, computers dot care much about bacteria used in the experiment so as long as we follow the same pathway, we only need to rename variables. Bless!<br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math's, as Rachel and Kristin does some analytical derivations for our model's optimization. To be honest, we were very optimistic about the outcome, and though, the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack, even for MatLAB. <br><br />
<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done by Maciej.<br><br />
<br />
== Week 3 ==<br />
=== 16/07 ===<br />
Glasgow Bank Holiday.<br />
<br />
=== 17/07 ===<br />
We were given a brief introduction to Bionessie and SBML. Also we be begun to get to grips with Global Sensitivity analysis.<br />
<br />
=== 18/07 ===<br />
A brief overview of SimBiology was given to the drylab by Gary. Martina and Rachel continued learning about Stochastic modelling, while the rest of the team were working on Sensitivity Analysis.<br />
<br />
=== 19/07 ===<br />
A presentation was given to both, the wetlab and the drylab, about the Full Text Fetcher programme which, will help to search and retrive research articles.<br />
The Stochastic Simulation Algorithm (Gillespie's algorithm) is yet ready in the code to run some stochastics simulations on the Michaelis_Menten system.<br />
<br />
=== 20/07 ===<br />
Today we realized that, we missed few important details in our model 1. All morning was like one big mess. Everybody gave their ideas how things should be sorted. <br />
Eventually, we settled our brainstormed ideas on board and decided to leave simulations for Monday because new parameter hunt for model 1.2 was about to begin…<br />
Stochastic's work keeps on fitting the fano factor!<br />
<br />
== Week 4 ==<br />
=== 23/07 ===<br />
Day spent on long discussions with Raya about the accuracy of our model 1.2 . We finally simulated it and… Results were a bit, shall I say, unpleasant. Because of signal degradation, we will not reach a stable state as we anticipated before. That is going to mess up our optimization algorithms, for sure.<br />
<br />
=== 24/07 ===<br />
Kristin was asked by Xu to introduce Petri Net([http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html Snoopy]) method to qualitatively analyse the dynamics of the system. And Karolis, introduced a dynamical approach in modeling of the system using Simulink. Both methods rely not only on blunt programming, but introduce GUI (Graphical User Interface) logics. Respect the Stochastic Model, we have been runing this one by doing some changes in the model (like changes in the signal, or other implementations), and later comparing with the deterministic model the results.<br />
<br />
=== 25/07 ===<br />
Maciek started a thorough research of registry files, because we were told by dry lab, that they are about to deposit their first brick and, it is not very intuitive (a good point for registry’s future development). He promised to study it and give us all tutorial about his findings. We have discussed as well about how we will determinate the parameters for the stochastic model.<br />
<br />
=== 26/07 ===<br />
Bricks. Brick Bricks. What is this brick? What is the aim of having bricks? All these questions were brought forward and we all agreed to do a thorough individual research and combine them in joint brainstorm, because as our grandfathers used to say: ‘There are as many opinions, as there are heads’. Reachel and Martina continue working in cascade models for Stochastics.<br />
<br />
=== 27/07 ===<br />
First bricks from Glasgow team reached a sandpit. No no. Do not rush to copy them. That’s just a ‘getting used to the system’. We are about to deposit real one, so we want everything to go as smooth as possible.<br />
<br />
== Week 5 ==<br />
=== 30/07 ===<br />
Maciek’s tutorial enlightened wet and dry labs about all the registry’s pluses and minuses. We now know how to deposit a brick, edit it and etc. During this tutorial, we compiled a list of ides and suggestions, how to update the concept of brick itself, and some suggestions for registry’s future. Some questions have been asked by Rachael to the weblab to do some changes in the stochastic model.<br />
<br />
=== 31/07 ===<br />
To pursue the further ideas about Brick-Based system modeling Karolis introduced some CAD techniqes for possible GUI algorithm and code development. Rach, beautiful plots about the fano factor!! ;)<br />
<br />
=== 01/08 ===<br />
When the day was about to be over, we received long awaited news… First experimental data have finally reached us. We will be able to do some curve fitting, parameter estimation and other cool stuff?<br />
<br />
=== 02/08 ===<br />
Today we brainstormed the data we have. Everybody added their bit to ideas pot, however, since the data wasn’t that plentiful as we expected, we queried wet-lab for some more input. They promised, that more data is on the way. Stochastics are runing the code for several numbers of cells, and it take long time to run those!<br />
<br />
=== 03/08 ===<br />
Friday. The end of week 5. Our project just passed major milestone. No, not in development, but in time left available for us to complete it. We are, officially, halfway to successes now?<br />
<br />
== Week 6 ==<br />
=== 06/08 ===<br />
Today we received extra data to support our estimations. General modelers meting raised issues like the further development of the model, feedback loops, or our possible influence for wet lab. Now, that we have some data, (input) we should produce some output for near future projects. Stochastics keep on runing simulations of data.<br />
<br />
=== 07/08 ===<br />
Day was full of events. First thing in the morning, we had a modelers meeting, to discuss our final model’s layout. General structure and equations were drafted on board. From now we will be analyzing previous data from lab and try to simulate new model, called Model F1. <br><br />
Edinburgh team came to visit us after lunch. We exchanged some ideas about project, including modeling approaches and wet lab techniques used. After a brief introduction, we decided to continue our conversation outside the lab, so went to check what Glasgow could offer us.<br />
<br />
=== 08/008 ===<br />
Most of the day spent on Model F1, Model F1 Fedback and Model F1 Constitutive. Discussion about the stochastics full model to be able to compared with the deterministic one.<br />
<br />
=== 09/08 ===<br />
Even more types of models have been suggested to simulate. We have so much data now, so in order to manage it, we decided to document everything in LATEX. General standards are agreed for all the constants and equation. These are to be officially published later on.<br />
<br />
=== 10/08 ===<br />
Today we realized, that even almighty MATLAB, is not always the best solution. Since our experiments require LHS (Latin Hypercube Sampling) in huge numbers and Matlab does it in one hour. We decided to switch back to Good Old C++. Job well done and in 10 SECONDS ONLY???!!!! What has just happened knows only Maciek himself. Only he knows The Way Of Gods.<br />
<br />
== Week 7 ==<br />
=== 13/08 ===<br />
The day was quite productive, nerveless lucky. We manage to find 3 parameters of our interest. Besides that, we came with idea, how to compare qualitatively models F2 and F3 feedback. The method we developed and called ‘Feedback Logics’ allowed us to optimize four unknowns in F3 feedback. Results that came out suggested that addition of feedback loop for F3 will not influence the outcome of *** (sorry classified). Tomorrows meeting will decide, if F3 is wrong or it is the outcome one could expect.<br />
<br />
=== 14/08 ===<br />
?<br />
=== 15/008 ===<br />
?<br />
=== 16/08 ===<br />
?<br />
=== 17/08 ===<br />
?</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-14T11:28:34Z<p>Freestym: /* 06/08 */</p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We were introduced to the 'Nested Functions' to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menten equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab, explaining the methods we employ, as modellers, to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took us an hour to finalize all the details. And now we have to go again.<br><br />
Lucky for us, modelers, computers dot care much about bacteria used in the experiment so as long as we follow the same pathway, we only need to rename variables. Bless!<br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math's, as Rachel and Kristin does some analytical derivations for our model's optimization. To be honest, we were very optimistic about the outcome, and though, the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack, even for MatLAB. <br><br />
<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done by Maciej.<br><br />
<br />
== Week 3 ==<br />
=== 16/07 ===<br />
Glasgow Bank Holiday.<br />
<br />
=== 17/07 ===<br />
We were given a brief introduction to Bionessie and SBML. Also we be begun to get to grips with Global Sensitivity analysis.<br />
<br />
=== 18/07 ===<br />
A brief overview of SimBiology was given to the drylab by Gary. Martina and Rachel continued learning about Stochastic modelling, while the rest of the team were working on Sensitivity Analysis.<br />
<br />
=== 19/07 ===<br />
A presentation was given to both, the wetlab and the drylab, about the Full Text Fetcher programme which, will help to search and retrive research articles.<br />
The Stochastic Simulation Algorithm (Gillespie's algorithm) is yet ready in the code to run some stochastics simulations on the Michaelis_Menten system.<br />
<br />
=== 20/07 ===<br />
Today we realized that, we missed few important details in our model 1. All morning was like one big mess. Everybody gave their ideas how things should be sorted. <br />
Eventually, we settled our brainstormed ideas on board and decided to leave simulations for Monday because new parameter hunt for model 1.2 was about to begin…<br />
Stochastic's work keeps on fitting the fano factor!<br />
<br />
== Week 4 ==<br />
=== 23/07 ===<br />
Day spent on long discussions with Raya about the accuracy of our model 1.2 . We finally simulated it and… Results were a bit, shall I say, unpleasant. Because of signal degradation, we will not reach a stable state as we anticipated before. That is going to mess up our optimization algorithms, for sure.<br />
<br />
=== 24/07 ===<br />
Kristin was asked by Xu to introduce Petri Net([http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html Snoopy]) method to qualitatively analyse the dynamics of the system. And Karolis, introduced a dynamical approach in modeling of the system using Simulink. Both methods rely not only on blunt programming, but introduce GUI (Graphical User Interface) logics. Respect the Stochastic Model, we have been runing this one by doing some changes in the model (like changes in the signal, or other implementations), and later comparing with the deterministic model the results.<br />
<br />
=== 25/07 ===<br />
Maciek started a thorough research of registry files, because we were told by dry lab, that they are about to deposit their first brick and, it is not very intuitive (a good point for registry’s future development). He promised to study it and give us all tutorial about his findings. We have discussed as well about how we will determinate the parameters for the stochastic model.<br />
<br />
=== 26/07 ===<br />
Bricks. Brick Bricks. What is this brick? What is the aim of having bricks? All these questions were brought forward and we all agreed to do a thorough individual research and combine them in joint brainstorm, because as our grandfathers used to say: ‘There are as many opinions, as there are heads’. Reachel and Martina continue working in cascade models for Stochastics.<br />
<br />
=== 27/07 ===<br />
First bricks from Glasgow team reached a sandpit. No no. Do not rush to copy them. That’s just a ‘getting used to the system’. We are about to deposit real one, so we want everything to go as smooth as possible.<br />
<br />
== Week 5 ==<br />
=== 30/07 ===<br />
Maciek’s tutorial enlightened wet and dry labs about all the registry’s pluses and minuses. We now know how to deposit a brick, edit it and etc. During this tutorial, we compiled a list of ides and suggestions, how to update the concept of brick itself, and some suggestions for registry’s future. Some questions have been asked by Rachael to the weblab to do some changes in the stochastic model.<br />
<br />
=== 31/07 ===<br />
To pursue the further ideas about Brick-Based system modeling Karolis introduced some CAD techniqes for possible GUI algorithm and code development. Rach, beautiful plots about the fano factor!! ;)<br />
<br />
=== 01/08 ===<br />
When the day was about to be over, we received long awaited news… First experimental data have finally reached us. We will be able to do some curve fitting, parameter estimation and other cool stuff?<br />
<br />
=== 02/08 ===<br />
Today we brainstormed the data we have. Everybody added their bit to ideas pot, however, since the data wasn’t that plentiful as we expected, we queried wet-lab for some more input. They promised, that more data is on the way. Stochastics are runing the code for several numbers of cells, and it take long time to run those!<br />
<br />
=== 03/08 ===<br />
Friday. The end of week 5. Our project just passed major milestone. No, not in development, but in time left available for us to complete it. We are, officially, halfway to successes now?<br />
<br />
== Week 6 ==<br />
=== 06/08 ===<br />
Today we received extra data to support our estimations. General modelers meting raised issues like the further development of the model, feedback loops, or our possible influence for wet lab. Now, that we have some data, (input) we should produce some output for near future projects. Stochastics keep on runing simulations of data.<br />
<br />
=== 07/08 ===<br />
Day was full of events. First thing in the morning, we had a modelers meeting, to discuss our final model’s layout. General structure and equations were drafted on board. From now we will be analyzing previous data from lab and try to simulate new model, called Model F1. <br><br />
Edinburgh team came to visit us after lunch. We exchanged some ideas about project, including modeling approaches and wet lab techniques used. After a brief introduction, we decided to continue our conversation outside the lab, so went to check what Glasgow could offer us.<br />
<br />
=== 08/008 ===<br />
Most of the day spent on Model F1, Model F1 Fedback and Model F1 Constitutive.<br />
<br />
=== 09/08 ===<br />
Even more types of models have been suggested to simulate. We have so much data now, so in order to manage it, we decided to document everything in LATEX. General standards are agreed for all the constants and equation. These are to be officially published later on.<br />
<br />
=== 10/08 ===<br />
Today we realized, that even almighty MATLAB, is not always the best solution. Since our experiments require LHS (Latin Hypercube Sampling) in huge numbers and Matlab does it in one hour. We decided to switch back to Good Old C++. Job well done and in 10 SECONDS ONLY???!!!! What has just happened knows only Maciek himself. Only he knows The Way Of Gods.<br />
<br />
== Week 7 ==<br />
=== 13/08 ===<br />
The day was quite productive, nerveless lucky. We manage to find 3 parameters of our interest. Besides that, we came with idea, how to compare qualitatively models F2 and F3 feedback. The method we developed and called ‘Feedback Logics’ allowed us to optimize four unknowns in F3 feedback. Results that came out suggested that addition of feedback loop for F3 will not influence the outcome of *** (sorry classified). Tomorrows meeting will decide, if F3 is wrong or it is the outcome one could expect.<br />
<br />
=== 14/08 ===<br />
?<br />
=== 15/008 ===<br />
?<br />
=== 16/08 ===<br />
?<br />
=== 17/08 ===<br />
?</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-14T11:27:23Z<p>Freestym: /* 02/08 */</p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We were introduced to the 'Nested Functions' to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menten equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab, explaining the methods we employ, as modellers, to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took us an hour to finalize all the details. And now we have to go again.<br><br />
Lucky for us, modelers, computers dot care much about bacteria used in the experiment so as long as we follow the same pathway, we only need to rename variables. Bless!<br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math's, as Rachel and Kristin does some analytical derivations for our model's optimization. To be honest, we were very optimistic about the outcome, and though, the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack, even for MatLAB. <br><br />
<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done by Maciej.<br><br />
<br />
== Week 3 ==<br />
=== 16/07 ===<br />
Glasgow Bank Holiday.<br />
<br />
=== 17/07 ===<br />
We were given a brief introduction to Bionessie and SBML. Also we be begun to get to grips with Global Sensitivity analysis.<br />
<br />
=== 18/07 ===<br />
A brief overview of SimBiology was given to the drylab by Gary. Martina and Rachel continued learning about Stochastic modelling, while the rest of the team were working on Sensitivity Analysis.<br />
<br />
=== 19/07 ===<br />
A presentation was given to both, the wetlab and the drylab, about the Full Text Fetcher programme which, will help to search and retrive research articles.<br />
The Stochastic Simulation Algorithm (Gillespie's algorithm) is yet ready in the code to run some stochastics simulations on the Michaelis_Menten system.<br />
<br />
=== 20/07 ===<br />
Today we realized that, we missed few important details in our model 1. All morning was like one big mess. Everybody gave their ideas how things should be sorted. <br />
Eventually, we settled our brainstormed ideas on board and decided to leave simulations for Monday because new parameter hunt for model 1.2 was about to begin…<br />
Stochastic's work keeps on fitting the fano factor!<br />
<br />
== Week 4 ==<br />
=== 23/07 ===<br />
Day spent on long discussions with Raya about the accuracy of our model 1.2 . We finally simulated it and… Results were a bit, shall I say, unpleasant. Because of signal degradation, we will not reach a stable state as we anticipated before. That is going to mess up our optimization algorithms, for sure.<br />
<br />
=== 24/07 ===<br />
Kristin was asked by Xu to introduce Petri Net([http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html Snoopy]) method to qualitatively analyse the dynamics of the system. And Karolis, introduced a dynamical approach in modeling of the system using Simulink. Both methods rely not only on blunt programming, but introduce GUI (Graphical User Interface) logics. Respect the Stochastic Model, we have been runing this one by doing some changes in the model (like changes in the signal, or other implementations), and later comparing with the deterministic model the results.<br />
<br />
=== 25/07 ===<br />
Maciek started a thorough research of registry files, because we were told by dry lab, that they are about to deposit their first brick and, it is not very intuitive (a good point for registry’s future development). He promised to study it and give us all tutorial about his findings. We have discussed as well about how we will determinate the parameters for the stochastic model.<br />
<br />
=== 26/07 ===<br />
Bricks. Brick Bricks. What is this brick? What is the aim of having bricks? All these questions were brought forward and we all agreed to do a thorough individual research and combine them in joint brainstorm, because as our grandfathers used to say: ‘There are as many opinions, as there are heads’. Reachel and Martina continue working in cascade models for Stochastics.<br />
<br />
=== 27/07 ===<br />
First bricks from Glasgow team reached a sandpit. No no. Do not rush to copy them. That’s just a ‘getting used to the system’. We are about to deposit real one, so we want everything to go as smooth as possible.<br />
<br />
== Week 5 ==<br />
=== 30/07 ===<br />
Maciek’s tutorial enlightened wet and dry labs about all the registry’s pluses and minuses. We now know how to deposit a brick, edit it and etc. During this tutorial, we compiled a list of ides and suggestions, how to update the concept of brick itself, and some suggestions for registry’s future. Some questions have been asked by Rachael to the weblab to do some changes in the stochastic model.<br />
<br />
=== 31/07 ===<br />
To pursue the further ideas about Brick-Based system modeling Karolis introduced some CAD techniqes for possible GUI algorithm and code development. Rach, beautiful plots about the fano factor!! ;)<br />
<br />
=== 01/08 ===<br />
When the day was about to be over, we received long awaited news… First experimental data have finally reached us. We will be able to do some curve fitting, parameter estimation and other cool stuff?<br />
<br />
=== 02/08 ===<br />
Today we brainstormed the data we have. Everybody added their bit to ideas pot, however, since the data wasn’t that plentiful as we expected, we queried wet-lab for some more input. They promised, that more data is on the way. Stochastics are runing the code for several numbers of cells, and it take long time to run those!<br />
<br />
=== 03/08 ===<br />
Friday. The end of week 5. Our project just passed major milestone. No, not in development, but in time left available for us to complete it. We are, officially, halfway to successes now?<br />
<br />
== Week 6 ==<br />
=== 06/08 ===<br />
Today we received extra data to support our estimations. General modelers meting raised issues like the further development of the model, feedback loops, or our possible influence for wet lab. Now, that we have some data, (input) we should produce some output for near future projects.<br />
<br />
=== 07/08 ===<br />
Day was full of events. First thing in the morning, we had a modelers meeting, to discuss our final model’s layout. General structure and equations were drafted on board. From now we will be analyzing previous data from lab and try to simulate new model, called Model F1. <br><br />
Edinburgh team came to visit us after lunch. We exchanged some ideas about project, including modeling approaches and wet lab techniques used. After a brief introduction, we decided to continue our conversation outside the lab, so went to check what Glasgow could offer us.<br />
<br />
=== 08/008 ===<br />
Most of the day spent on Model F1, Model F1 Fedback and Model F1 Constitutive.<br />
<br />
=== 09/08 ===<br />
Even more types of models have been suggested to simulate. We have so much data now, so in order to manage it, we decided to document everything in LATEX. General standards are agreed for all the constants and equation. These are to be officially published later on.<br />
<br />
=== 10/08 ===<br />
Today we realized, that even almighty MATLAB, is not always the best solution. Since our experiments require LHS (Latin Hypercube Sampling) in huge numbers and Matlab does it in one hour. We decided to switch back to Good Old C++. Job well done and in 10 SECONDS ONLY???!!!! What has just happened knows only Maciek himself. Only he knows The Way Of Gods.<br />
<br />
== Week 7 ==<br />
=== 13/08 ===<br />
The day was quite productive, nerveless lucky. We manage to find 3 parameters of our interest. Besides that, we came with idea, how to compare qualitatively models F2 and F3 feedback. The method we developed and called ‘Feedback Logics’ allowed us to optimize four unknowns in F3 feedback. Results that came out suggested that addition of feedback loop for F3 will not influence the outcome of *** (sorry classified). Tomorrows meeting will decide, if F3 is wrong or it is the outcome one could expect.<br />
<br />
=== 14/08 ===<br />
?<br />
=== 15/008 ===<br />
?<br />
=== 16/08 ===<br />
?<br />
=== 17/08 ===<br />
?</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-14T11:25:08Z<p>Freestym: /* 31/07 */</p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We were introduced to the 'Nested Functions' to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menten equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab, explaining the methods we employ, as modellers, to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took us an hour to finalize all the details. And now we have to go again.<br><br />
Lucky for us, modelers, computers dot care much about bacteria used in the experiment so as long as we follow the same pathway, we only need to rename variables. Bless!<br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math's, as Rachel and Kristin does some analytical derivations for our model's optimization. To be honest, we were very optimistic about the outcome, and though, the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack, even for MatLAB. <br><br />
<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done by Maciej.<br><br />
<br />
== Week 3 ==<br />
=== 16/07 ===<br />
Glasgow Bank Holiday.<br />
<br />
=== 17/07 ===<br />
We were given a brief introduction to Bionessie and SBML. Also we be begun to get to grips with Global Sensitivity analysis.<br />
<br />
=== 18/07 ===<br />
A brief overview of SimBiology was given to the drylab by Gary. Martina and Rachel continued learning about Stochastic modelling, while the rest of the team were working on Sensitivity Analysis.<br />
<br />
=== 19/07 ===<br />
A presentation was given to both, the wetlab and the drylab, about the Full Text Fetcher programme which, will help to search and retrive research articles.<br />
The Stochastic Simulation Algorithm (Gillespie's algorithm) is yet ready in the code to run some stochastics simulations on the Michaelis_Menten system.<br />
<br />
=== 20/07 ===<br />
Today we realized that, we missed few important details in our model 1. All morning was like one big mess. Everybody gave their ideas how things should be sorted. <br />
Eventually, we settled our brainstormed ideas on board and decided to leave simulations for Monday because new parameter hunt for model 1.2 was about to begin…<br />
Stochastic's work keeps on fitting the fano factor!<br />
<br />
== Week 4 ==<br />
=== 23/07 ===<br />
Day spent on long discussions with Raya about the accuracy of our model 1.2 . We finally simulated it and… Results were a bit, shall I say, unpleasant. Because of signal degradation, we will not reach a stable state as we anticipated before. That is going to mess up our optimization algorithms, for sure.<br />
<br />
=== 24/07 ===<br />
Kristin was asked by Xu to introduce Petri Net([http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html Snoopy]) method to qualitatively analyse the dynamics of the system. And Karolis, introduced a dynamical approach in modeling of the system using Simulink. Both methods rely not only on blunt programming, but introduce GUI (Graphical User Interface) logics. Respect the Stochastic Model, we have been runing this one by doing some changes in the model (like changes in the signal, or other implementations), and later comparing with the deterministic model the results.<br />
<br />
=== 25/07 ===<br />
Maciek started a thorough research of registry files, because we were told by dry lab, that they are about to deposit their first brick and, it is not very intuitive (a good point for registry’s future development). He promised to study it and give us all tutorial about his findings. We have discussed as well about how we will determinate the parameters for the stochastic model.<br />
<br />
=== 26/07 ===<br />
Bricks. Brick Bricks. What is this brick? What is the aim of having bricks? All these questions were brought forward and we all agreed to do a thorough individual research and combine them in joint brainstorm, because as our grandfathers used to say: ‘There are as many opinions, as there are heads’. Reachel and Martina continue working in cascade models for Stochastics.<br />
<br />
=== 27/07 ===<br />
First bricks from Glasgow team reached a sandpit. No no. Do not rush to copy them. That’s just a ‘getting used to the system’. We are about to deposit real one, so we want everything to go as smooth as possible.<br />
<br />
== Week 5 ==<br />
=== 30/07 ===<br />
Maciek’s tutorial enlightened wet and dry labs about all the registry’s pluses and minuses. We now know how to deposit a brick, edit it and etc. During this tutorial, we compiled a list of ides and suggestions, how to update the concept of brick itself, and some suggestions for registry’s future. Some questions have been asked by Rachael to the weblab to do some changes in the stochastic model.<br />
<br />
=== 31/07 ===<br />
To pursue the further ideas about Brick-Based system modeling Karolis introduced some CAD techniqes for possible GUI algorithm and code development. Rach, beautiful plots about the fano factor!! ;)<br />
<br />
=== 01/08 ===<br />
When the day was about to be over, we received long awaited news… First experimental data have finally reached us. We will be able to do some curve fitting, parameter estimation and other cool stuff?<br />
<br />
=== 02/08 ===<br />
Today we brainstormed the data we have. Everybody added their bit to ideas pot, however, since the data wasn’t that plentiful as we expected, we queried wet-lab for some more input. They promised, that more data is on the way.<br />
<br />
=== 03/08 ===<br />
Friday. The end of week 5. Our project just passed major milestone. No, not in development, but in time left available for us to complete it. We are, officially, halfway to successes now?<br />
<br />
== Week 6 ==<br />
=== 06/08 ===<br />
Today we received extra data to support our estimations. General modelers meting raised issues like the further development of the model, feedback loops, or our possible influence for wet lab. Now, that we have some data, (input) we should produce some output for near future projects.<br />
<br />
=== 07/08 ===<br />
Day was full of events. First thing in the morning, we had a modelers meeting, to discuss our final model’s layout. General structure and equations were drafted on board. From now we will be analyzing previous data from lab and try to simulate new model, called Model F1. <br><br />
Edinburgh team came to visit us after lunch. We exchanged some ideas about project, including modeling approaches and wet lab techniques used. After a brief introduction, we decided to continue our conversation outside the lab, so went to check what Glasgow could offer us.<br />
<br />
=== 08/008 ===<br />
Most of the day spent on Model F1, Model F1 Fedback and Model F1 Constitutive.<br />
<br />
=== 09/08 ===<br />
Even more types of models have been suggested to simulate. We have so much data now, so in order to manage it, we decided to document everything in LATEX. General standards are agreed for all the constants and equation. These are to be officially published later on.<br />
<br />
=== 10/08 ===<br />
Today we realized, that even almighty MATLAB, is not always the best solution. Since our experiments require LHS (Latin Hypercube Sampling) in huge numbers and Matlab does it in one hour. We decided to switch back to Good Old C++. Job well done and in 10 SECONDS ONLY???!!!! What has just happened knows only Maciek himself. Only he knows The Way Of Gods.<br />
<br />
== Week 7 ==<br />
=== 13/08 ===<br />
The day was quite productive, nerveless lucky. We manage to find 3 parameters of our interest. Besides that, we came with idea, how to compare qualitatively models F2 and F3 feedback. The method we developed and called ‘Feedback Logics’ allowed us to optimize four unknowns in F3 feedback. Results that came out suggested that addition of feedback loop for F3 will not influence the outcome of *** (sorry classified). Tomorrows meeting will decide, if F3 is wrong or it is the outcome one could expect.<br />
<br />
=== 14/08 ===<br />
?<br />
=== 15/008 ===<br />
?<br />
=== 16/08 ===<br />
?<br />
=== 17/08 ===<br />
?</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-14T11:24:24Z<p>Freestym: /* 30/07 */</p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We were introduced to the 'Nested Functions' to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menten equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab, explaining the methods we employ, as modellers, to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took us an hour to finalize all the details. And now we have to go again.<br><br />
Lucky for us, modelers, computers dot care much about bacteria used in the experiment so as long as we follow the same pathway, we only need to rename variables. Bless!<br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math's, as Rachel and Kristin does some analytical derivations for our model's optimization. To be honest, we were very optimistic about the outcome, and though, the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack, even for MatLAB. <br><br />
<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done by Maciej.<br><br />
<br />
== Week 3 ==<br />
=== 16/07 ===<br />
Glasgow Bank Holiday.<br />
<br />
=== 17/07 ===<br />
We were given a brief introduction to Bionessie and SBML. Also we be begun to get to grips with Global Sensitivity analysis.<br />
<br />
=== 18/07 ===<br />
A brief overview of SimBiology was given to the drylab by Gary. Martina and Rachel continued learning about Stochastic modelling, while the rest of the team were working on Sensitivity Analysis.<br />
<br />
=== 19/07 ===<br />
A presentation was given to both, the wetlab and the drylab, about the Full Text Fetcher programme which, will help to search and retrive research articles.<br />
The Stochastic Simulation Algorithm (Gillespie's algorithm) is yet ready in the code to run some stochastics simulations on the Michaelis_Menten system.<br />
<br />
=== 20/07 ===<br />
Today we realized that, we missed few important details in our model 1. All morning was like one big mess. Everybody gave their ideas how things should be sorted. <br />
Eventually, we settled our brainstormed ideas on board and decided to leave simulations for Monday because new parameter hunt for model 1.2 was about to begin…<br />
Stochastic's work keeps on fitting the fano factor!<br />
<br />
== Week 4 ==<br />
=== 23/07 ===<br />
Day spent on long discussions with Raya about the accuracy of our model 1.2 . We finally simulated it and… Results were a bit, shall I say, unpleasant. Because of signal degradation, we will not reach a stable state as we anticipated before. That is going to mess up our optimization algorithms, for sure.<br />
<br />
=== 24/07 ===<br />
Kristin was asked by Xu to introduce Petri Net([http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html Snoopy]) method to qualitatively analyse the dynamics of the system. And Karolis, introduced a dynamical approach in modeling of the system using Simulink. Both methods rely not only on blunt programming, but introduce GUI (Graphical User Interface) logics. Respect the Stochastic Model, we have been runing this one by doing some changes in the model (like changes in the signal, or other implementations), and later comparing with the deterministic model the results.<br />
<br />
=== 25/07 ===<br />
Maciek started a thorough research of registry files, because we were told by dry lab, that they are about to deposit their first brick and, it is not very intuitive (a good point for registry’s future development). He promised to study it and give us all tutorial about his findings. We have discussed as well about how we will determinate the parameters for the stochastic model.<br />
<br />
=== 26/07 ===<br />
Bricks. Brick Bricks. What is this brick? What is the aim of having bricks? All these questions were brought forward and we all agreed to do a thorough individual research and combine them in joint brainstorm, because as our grandfathers used to say: ‘There are as many opinions, as there are heads’. Reachel and Martina continue working in cascade models for Stochastics.<br />
<br />
=== 27/07 ===<br />
First bricks from Glasgow team reached a sandpit. No no. Do not rush to copy them. That’s just a ‘getting used to the system’. We are about to deposit real one, so we want everything to go as smooth as possible.<br />
<br />
== Week 5 ==<br />
=== 30/07 ===<br />
Maciek’s tutorial enlightened wet and dry labs about all the registry’s pluses and minuses. We now know how to deposit a brick, edit it and etc. During this tutorial, we compiled a list of ides and suggestions, how to update the concept of brick itself, and some suggestions for registry’s future. Some questions have been asked by Rachael to the weblab to do some changes in the stochastic model.<br />
<br />
=== 31/07 ===<br />
To pursue the further ideas about Brick-Based system modeling Karolis introduced some CAD techniqes for possible GUI algorithm and code development.<br />
<br />
=== 01/08 ===<br />
When the day was about to be over, we received long awaited news… First experimental data have finally reached us. We will be able to do some curve fitting, parameter estimation and other cool stuff?<br />
<br />
=== 02/08 ===<br />
Today we brainstormed the data we have. Everybody added their bit to ideas pot, however, since the data wasn’t that plentiful as we expected, we queried wet-lab for some more input. They promised, that more data is on the way.<br />
<br />
=== 03/08 ===<br />
Friday. The end of week 5. Our project just passed major milestone. No, not in development, but in time left available for us to complete it. We are, officially, halfway to successes now?<br />
<br />
== Week 6 ==<br />
=== 06/08 ===<br />
Today we received extra data to support our estimations. General modelers meting raised issues like the further development of the model, feedback loops, or our possible influence for wet lab. Now, that we have some data, (input) we should produce some output for near future projects.<br />
<br />
=== 07/08 ===<br />
Day was full of events. First thing in the morning, we had a modelers meeting, to discuss our final model’s layout. General structure and equations were drafted on board. From now we will be analyzing previous data from lab and try to simulate new model, called Model F1. <br><br />
Edinburgh team came to visit us after lunch. We exchanged some ideas about project, including modeling approaches and wet lab techniques used. After a brief introduction, we decided to continue our conversation outside the lab, so went to check what Glasgow could offer us.<br />
<br />
=== 08/008 ===<br />
Most of the day spent on Model F1, Model F1 Fedback and Model F1 Constitutive.<br />
<br />
=== 09/08 ===<br />
Even more types of models have been suggested to simulate. We have so much data now, so in order to manage it, we decided to document everything in LATEX. General standards are agreed for all the constants and equation. These are to be officially published later on.<br />
<br />
=== 10/08 ===<br />
Today we realized, that even almighty MATLAB, is not always the best solution. Since our experiments require LHS (Latin Hypercube Sampling) in huge numbers and Matlab does it in one hour. We decided to switch back to Good Old C++. Job well done and in 10 SECONDS ONLY???!!!! What has just happened knows only Maciek himself. Only he knows The Way Of Gods.<br />
<br />
== Week 7 ==<br />
=== 13/08 ===<br />
The day was quite productive, nerveless lucky. We manage to find 3 parameters of our interest. Besides that, we came with idea, how to compare qualitatively models F2 and F3 feedback. The method we developed and called ‘Feedback Logics’ allowed us to optimize four unknowns in F3 feedback. Results that came out suggested that addition of feedback loop for F3 will not influence the outcome of *** (sorry classified). Tomorrows meeting will decide, if F3 is wrong or it is the outcome one could expect.<br />
<br />
=== 14/08 ===<br />
?<br />
=== 15/008 ===<br />
?<br />
=== 16/08 ===<br />
?<br />
=== 17/08 ===<br />
?</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-14T11:24:02Z<p>Freestym: /* 30/07 */</p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We were introduced to the 'Nested Functions' to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menten equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab, explaining the methods we employ, as modellers, to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took us an hour to finalize all the details. And now we have to go again.<br><br />
Lucky for us, modelers, computers dot care much about bacteria used in the experiment so as long as we follow the same pathway, we only need to rename variables. Bless!<br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math's, as Rachel and Kristin does some analytical derivations for our model's optimization. To be honest, we were very optimistic about the outcome, and though, the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack, even for MatLAB. <br><br />
<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done by Maciej.<br><br />
<br />
== Week 3 ==<br />
=== 16/07 ===<br />
Glasgow Bank Holiday.<br />
<br />
=== 17/07 ===<br />
We were given a brief introduction to Bionessie and SBML. Also we be begun to get to grips with Global Sensitivity analysis.<br />
<br />
=== 18/07 ===<br />
A brief overview of SimBiology was given to the drylab by Gary. Martina and Rachel continued learning about Stochastic modelling, while the rest of the team were working on Sensitivity Analysis.<br />
<br />
=== 19/07 ===<br />
A presentation was given to both, the wetlab and the drylab, about the Full Text Fetcher programme which, will help to search and retrive research articles.<br />
The Stochastic Simulation Algorithm (Gillespie's algorithm) is yet ready in the code to run some stochastics simulations on the Michaelis_Menten system.<br />
<br />
=== 20/07 ===<br />
Today we realized that, we missed few important details in our model 1. All morning was like one big mess. Everybody gave their ideas how things should be sorted. <br />
Eventually, we settled our brainstormed ideas on board and decided to leave simulations for Monday because new parameter hunt for model 1.2 was about to begin…<br />
Stochastic's work keeps on fitting the fano factor!<br />
<br />
== Week 4 ==<br />
=== 23/07 ===<br />
Day spent on long discussions with Raya about the accuracy of our model 1.2 . We finally simulated it and… Results were a bit, shall I say, unpleasant. Because of signal degradation, we will not reach a stable state as we anticipated before. That is going to mess up our optimization algorithms, for sure.<br />
<br />
=== 24/07 ===<br />
Kristin was asked by Xu to introduce Petri Net([http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html Snoopy]) method to qualitatively analyse the dynamics of the system. And Karolis, introduced a dynamical approach in modeling of the system using Simulink. Both methods rely not only on blunt programming, but introduce GUI (Graphical User Interface) logics. Respect the Stochastic Model, we have been runing this one by doing some changes in the model (like changes in the signal, or other implementations), and later comparing with the deterministic model the results.<br />
<br />
=== 25/07 ===<br />
Maciek started a thorough research of registry files, because we were told by dry lab, that they are about to deposit their first brick and, it is not very intuitive (a good point for registry’s future development). He promised to study it and give us all tutorial about his findings. We have discussed as well about how we will determinate the parameters for the stochastic model.<br />
<br />
=== 26/07 ===<br />
Bricks. Brick Bricks. What is this brick? What is the aim of having bricks? All these questions were brought forward and we all agreed to do a thorough individual research and combine them in joint brainstorm, because as our grandfathers used to say: ‘There are as many opinions, as there are heads’. Reachel and Martina continue working in cascade models for Stochastics.<br />
<br />
=== 27/07 ===<br />
First bricks from Glasgow team reached a sandpit. No no. Do not rush to copy them. That’s just a ‘getting used to the system’. We are about to deposit real one, so we want everything to go as smooth as possible.<br />
<br />
== Week 5 ==<br />
=== 30/07 ===<br />
Maciek’s tutorial enlightened wet and dry labs about all the registry’s pluses and minuses. We now know how to deposit a brick, edit it and etc. During this tutorial, we compiled a list of ides and suggestions, how to update the concept of brick itself, and some suggestions for registry’s future. Some questions have been asked by Rachael to the weblab to do some changes in the stochastic model. Nice plots about the fano factor Rach!!<br />
<br />
=== 31/07 ===<br />
To pursue the further ideas about Brick-Based system modeling Karolis introduced some CAD techniqes for possible GUI algorithm and code development.<br />
<br />
=== 01/08 ===<br />
When the day was about to be over, we received long awaited news… First experimental data have finally reached us. We will be able to do some curve fitting, parameter estimation and other cool stuff?<br />
<br />
=== 02/08 ===<br />
Today we brainstormed the data we have. Everybody added their bit to ideas pot, however, since the data wasn’t that plentiful as we expected, we queried wet-lab for some more input. They promised, that more data is on the way.<br />
<br />
=== 03/08 ===<br />
Friday. The end of week 5. Our project just passed major milestone. No, not in development, but in time left available for us to complete it. We are, officially, halfway to successes now?<br />
<br />
== Week 6 ==<br />
=== 06/08 ===<br />
Today we received extra data to support our estimations. General modelers meting raised issues like the further development of the model, feedback loops, or our possible influence for wet lab. Now, that we have some data, (input) we should produce some output for near future projects.<br />
<br />
=== 07/08 ===<br />
Day was full of events. First thing in the morning, we had a modelers meeting, to discuss our final model’s layout. General structure and equations were drafted on board. From now we will be analyzing previous data from lab and try to simulate new model, called Model F1. <br><br />
Edinburgh team came to visit us after lunch. We exchanged some ideas about project, including modeling approaches and wet lab techniques used. After a brief introduction, we decided to continue our conversation outside the lab, so went to check what Glasgow could offer us.<br />
<br />
=== 08/008 ===<br />
Most of the day spent on Model F1, Model F1 Fedback and Model F1 Constitutive.<br />
<br />
=== 09/08 ===<br />
Even more types of models have been suggested to simulate. We have so much data now, so in order to manage it, we decided to document everything in LATEX. General standards are agreed for all the constants and equation. These are to be officially published later on.<br />
<br />
=== 10/08 ===<br />
Today we realized, that even almighty MATLAB, is not always the best solution. Since our experiments require LHS (Latin Hypercube Sampling) in huge numbers and Matlab does it in one hour. We decided to switch back to Good Old C++. Job well done and in 10 SECONDS ONLY???!!!! What has just happened knows only Maciek himself. Only he knows The Way Of Gods.<br />
<br />
== Week 7 ==<br />
=== 13/08 ===<br />
The day was quite productive, nerveless lucky. We manage to find 3 parameters of our interest. Besides that, we came with idea, how to compare qualitatively models F2 and F3 feedback. The method we developed and called ‘Feedback Logics’ allowed us to optimize four unknowns in F3 feedback. Results that came out suggested that addition of feedback loop for F3 will not influence the outcome of *** (sorry classified). Tomorrows meeting will decide, if F3 is wrong or it is the outcome one could expect.<br />
<br />
=== 14/08 ===<br />
?<br />
=== 15/008 ===<br />
?<br />
=== 16/08 ===<br />
?<br />
=== 17/08 ===<br />
?</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-14T11:19:05Z<p>Freestym: /* 24/07 */</p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We were introduced to the 'Nested Functions' to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menten equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab, explaining the methods we employ, as modellers, to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took us an hour to finalize all the details. And now we have to go again.<br><br />
Lucky for us, modelers, computers dot care much about bacteria used in the experiment so as long as we follow the same pathway, we only need to rename variables. Bless!<br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math's, as Rachel and Kristin does some analytical derivations for our model's optimization. To be honest, we were very optimistic about the outcome, and though, the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack, even for MatLAB. <br><br />
<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done by Maciej.<br><br />
<br />
== Week 3 ==<br />
=== 16/07 ===<br />
Glasgow Bank Holiday.<br />
<br />
=== 17/07 ===<br />
We were given a brief introduction to Bionessie and SBML. Also we be begun to get to grips with Global Sensitivity analysis.<br />
<br />
=== 18/07 ===<br />
A brief overview of SimBiology was given to the drylab by Gary. Martina and Rachel continued learning about Stochastic modelling, while the rest of the team were working on Sensitivity Analysis.<br />
<br />
=== 19/07 ===<br />
A presentation was given to both, the wetlab and the drylab, about the Full Text Fetcher programme which, will help to search and retrive research articles.<br />
The Stochastic Simulation Algorithm (Gillespie's algorithm) is yet ready in the code to run some stochastics simulations on the Michaelis_Menten system.<br />
<br />
=== 20/07 ===<br />
Today we realized that, we missed few important details in our model 1. All morning was like one big mess. Everybody gave their ideas how things should be sorted. <br />
Eventually, we settled our brainstormed ideas on board and decided to leave simulations for Monday because new parameter hunt for model 1.2 was about to begin…<br />
Stochastic's work keeps on fitting the fano factor!<br />
<br />
== Week 4 ==<br />
=== 23/07 ===<br />
Day spent on long discussions with Raya about the accuracy of our model 1.2 . We finally simulated it and… Results were a bit, shall I say, unpleasant. Because of signal degradation, we will not reach a stable state as we anticipated before. That is going to mess up our optimization algorithms, for sure.<br />
<br />
=== 24/07 ===<br />
Kristin was asked by Xu to introduce Petri Net([http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html Snoopy]) method to qualitatively analyse the dynamics of the system. And Karolis, introduced a dynamical approach in modeling of the system using Simulink. Both methods rely not only on blunt programming, but introduce GUI (Graphical User Interface) logics. Respect the Stochastic Model, we have been runing this one by doing some changes in the model (like changes in the signal, or other implementations), and later comparing with the deterministic model the results.<br />
<br />
=== 25/07 ===<br />
Maciek started a thorough research of registry files, because we were told by dry lab, that they are about to deposit their first brick and, it is not very intuitive (a good point for registry’s future development). He promised to study it and give us all tutorial about his findings. We have discussed as well about how we will determinate the parameters for the stochastic model.<br />
<br />
=== 26/07 ===<br />
Bricks. Brick Bricks. What is this brick? What is the aim of having bricks? All these questions were brought forward and we all agreed to do a thorough individual research and combine them in joint brainstorm, because as our grandfathers used to say: ‘There are as many opinions, as there are heads’. Reachel and Martina continue working in cascade models for Stochastics.<br />
<br />
=== 27/07 ===<br />
First bricks from Glasgow team reached a sandpit. No no. Do not rush to copy them. That’s just a ‘getting used to the system’. We are about to deposit real one, so we want everything to go as smooth as possible.<br />
<br />
== Week 5 ==<br />
=== 30/07 ===<br />
Maciek’s tutorial enlightened wet and dry labs about all the registry’s pluses and minuses. We now know how to deposit a brick, edit it and etc. During this tutorial, we compiled a list of ides and suggestions, how to update the concept of brick itself, and some suggestions for registry’s future.<br />
<br />
=== 31/07 ===<br />
To pursue the further ideas about Brick-Based system modeling Karolis introduced some CAD techniqes for possible GUI algorithm and code development.<br />
<br />
=== 01/08 ===<br />
When the day was about to be over, we received long awaited news… First experimental data have finally reached us. We will be able to do some curve fitting, parameter estimation and other cool stuff?<br />
<br />
=== 02/08 ===<br />
Today we brainstormed the data we have. Everybody added their bit to ideas pot, however, since the data wasn’t that plentiful as we expected, we queried wet-lab for some more input. They promised, that more data is on the way.<br />
<br />
=== 03/08 ===<br />
Friday. The end of week 5. Our project just passed major milestone. No, not in development, but in time left available for us to complete it. We are, officially, halfway to successes now?<br />
<br />
== Week 6 ==<br />
=== 06/08 ===<br />
Today we received extra data to support our estimations. General modelers meting raised issues like the further development of the model, feedback loops, or our possible influence for wet lab. Now, that we have some data, (input) we should produce some output for near future projects.<br />
<br />
=== 07/08 ===<br />
Day was full of events. First thing in the morning, we had a modelers meeting, to discuss our final model’s layout. General structure and equations were drafted on board. From now we will be analyzing previous data from lab and try to simulate new model, called Model F1. <br><br />
Edinburgh team came to visit us after lunch. We exchanged some ideas about project, including modeling approaches and wet lab techniques used. After a brief introduction, we decided to continue our conversation outside the lab, so went to check what Glasgow could offer us.<br />
<br />
=== 08/008 ===<br />
Most of the day spent on Model F1, Model F1 Fedback and Model F1 Constitutive.<br />
<br />
=== 09/08 ===<br />
Even more types of models have been suggested to simulate. We have so much data now, so in order to manage it, we decided to document everything in LATEX. General standards are agreed for all the constants and equation. These are to be officially published later on.<br />
<br />
=== 10/08 ===<br />
Today we realized, that even almighty MATLAB, is not always the best solution. Since our experiments require LHS (Latin Hypercube Sampling) in huge numbers and Matlab does it in one hour. We decided to switch back to Good Old C++. Job well done and in 10 SECONDS ONLY???!!!! What has just happened knows only Maciek himself. Only he knows The Way Of Gods.<br />
<br />
== Week 7 ==<br />
=== 13/08 ===<br />
The day was quite productive, nerveless lucky. We manage to find 3 parameters of our interest. Besides that, we came with idea, how to compare qualitatively models F2 and F3 feedback. The method we developed and called ‘Feedback Logics’ allowed us to optimize four unknowns in F3 feedback. Results that came out suggested that addition of feedback loop for F3 will not influence the outcome of *** (sorry classified). Tomorrows meeting will decide, if F3 is wrong or it is the outcome one could expect.<br />
<br />
=== 14/08 ===<br />
?<br />
=== 15/008 ===<br />
?<br />
=== 16/08 ===<br />
?<br />
=== 17/08 ===<br />
?</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-14T11:15:43Z<p>Freestym: /* 25/07 */</p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We were introduced to the 'Nested Functions' to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menten equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab, explaining the methods we employ, as modellers, to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took us an hour to finalize all the details. And now we have to go again.<br><br />
Lucky for us, modelers, computers dot care much about bacteria used in the experiment so as long as we follow the same pathway, we only need to rename variables. Bless!<br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math's, as Rachel and Kristin does some analytical derivations for our model's optimization. To be honest, we were very optimistic about the outcome, and though, the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack, even for MatLAB. <br><br />
<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done by Maciej.<br><br />
<br />
== Week 3 ==<br />
=== 16/07 ===<br />
Glasgow Bank Holiday.<br />
<br />
=== 17/07 ===<br />
We were given a brief introduction to Bionessie and SBML. Also we be begun to get to grips with Global Sensitivity analysis.<br />
<br />
=== 18/07 ===<br />
A brief overview of SimBiology was given to the drylab by Gary. Martina and Rachel continued learning about Stochastic modelling, while the rest of the team were working on Sensitivity Analysis.<br />
<br />
=== 19/07 ===<br />
A presentation was given to both, the wetlab and the drylab, about the Full Text Fetcher programme which, will help to search and retrive research articles.<br />
The Stochastic Simulation Algorithm (Gillespie's algorithm) is yet ready in the code to run some stochastics simulations on the Michaelis_Menten system.<br />
<br />
=== 20/07 ===<br />
Today we realized that, we missed few important details in our model 1. All morning was like one big mess. Everybody gave their ideas how things should be sorted. <br />
Eventually, we settled our brainstormed ideas on board and decided to leave simulations for Monday because new parameter hunt for model 1.2 was about to begin…<br />
Stochastic's work keeps on fitting the fano factor!<br />
<br />
== Week 4 ==<br />
=== 23/07 ===<br />
Day spent on long discussions with Raya about the accuracy of our model 1.2 . We finally simulated it and… Results were a bit, shall I say, unpleasant. Because of signal degradation, we will not reach a stable state as we anticipated before. That is going to mess up our optimization algorithms, for sure.<br />
<br />
=== 24/07 ===<br />
Kristin was asked by Xu to introduce Petri Net([http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html Snoopy]) method to qualitatively analyse the dynamics of the system. And Karolis, introduced a dynamical approach in modeling of the system using Simulink. Both methods rely not only on blunt programming, but introduce GUI (Graphical User Interface) logics. Respect the Stochastic Model, we are trying to run this one by doing some changes in the model (like changes in the signal, or other implementations).<br />
<br />
=== 25/07 ===<br />
Maciek started a thorough research of registry files, because we were told by dry lab, that they are about to deposit their first brick and, it is not very intuitive (a good point for registry’s future development). He promised to study it and give us all tutorial about his findings. We have discussed as well about how we will determinate the parameters for the stochastic model.<br />
<br />
=== 26/07 ===<br />
Bricks. Brick Bricks. What is this brick? What is the aim of having bricks? All these questions were brought forward and we all agreed to do a thorough individual research and combine them in joint brainstorm, because as our grandfathers used to say: ‘There are as many opinions, as there are heads’. Reachel and Martina continue working in cascade models for Stochastics.<br />
<br />
=== 27/07 ===<br />
First bricks from Glasgow team reached a sandpit. No no. Do not rush to copy them. That’s just a ‘getting used to the system’. We are about to deposit real one, so we want everything to go as smooth as possible.<br />
<br />
== Week 5 ==<br />
=== 30/07 ===<br />
Maciek’s tutorial enlightened wet and dry labs about all the registry’s pluses and minuses. We now know how to deposit a brick, edit it and etc. During this tutorial, we compiled a list of ides and suggestions, how to update the concept of brick itself, and some suggestions for registry’s future.<br />
<br />
=== 31/07 ===<br />
To pursue the further ideas about Brick-Based system modeling Karolis introduced some CAD techniqes for possible GUI algorithm and code development.<br />
<br />
=== 01/08 ===<br />
When the day was about to be over, we received long awaited news… First experimental data have finally reached us. We will be able to do some curve fitting, parameter estimation and other cool stuff?<br />
<br />
=== 02/08 ===<br />
Today we brainstormed the data we have. Everybody added their bit to ideas pot, however, since the data wasn’t that plentiful as we expected, we queried wet-lab for some more input. They promised, that more data is on the way.<br />
<br />
=== 03/08 ===<br />
Friday. The end of week 5. Our project just passed major milestone. No, not in development, but in time left available for us to complete it. We are, officially, halfway to successes now?<br />
<br />
== Week 6 ==<br />
=== 06/08 ===<br />
Today we received extra data to support our estimations. General modelers meting raised issues like the further development of the model, feedback loops, or our possible influence for wet lab. Now, that we have some data, (input) we should produce some output for near future projects.<br />
<br />
=== 07/08 ===<br />
Day was full of events. First thing in the morning, we had a modelers meeting, to discuss our final model’s layout. General structure and equations were drafted on board. From now we will be analyzing previous data from lab and try to simulate new model, called Model F1. <br><br />
Edinburgh team came to visit us after lunch. We exchanged some ideas about project, including modeling approaches and wet lab techniques used. After a brief introduction, we decided to continue our conversation outside the lab, so went to check what Glasgow could offer us.<br />
<br />
=== 08/008 ===<br />
Most of the day spent on Model F1, Model F1 Fedback and Model F1 Constitutive.<br />
<br />
=== 09/08 ===<br />
Even more types of models have been suggested to simulate. We have so much data now, so in order to manage it, we decided to document everything in LATEX. General standards are agreed for all the constants and equation. These are to be officially published later on.<br />
<br />
=== 10/08 ===<br />
Today we realized, that even almighty MATLAB, is not always the best solution. Since our experiments require LHS (Latin Hypercube Sampling) in huge numbers and Matlab does it in one hour. We decided to switch back to Good Old C++. Job well done and in 10 SECONDS ONLY???!!!! What has just happened knows only Maciek himself. Only he knows The Way Of Gods.<br />
<br />
== Week 7 ==<br />
=== 13/08 ===<br />
The day was quite productive, nerveless lucky. We manage to find 3 parameters of our interest. Besides that, we came with idea, how to compare qualitatively models F2 and F3 feedback. The method we developed and called ‘Feedback Logics’ allowed us to optimize four unknowns in F3 feedback. Results that came out suggested that addition of feedback loop for F3 will not influence the outcome of *** (sorry classified). Tomorrows meeting will decide, if F3 is wrong or it is the outcome one could expect.<br />
<br />
=== 14/08 ===<br />
?<br />
=== 15/008 ===<br />
?<br />
=== 16/08 ===<br />
?<br />
=== 17/08 ===<br />
?</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-14T11:14:22Z<p>Freestym: /* 26/07 */</p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We were introduced to the 'Nested Functions' to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menten equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab, explaining the methods we employ, as modellers, to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took us an hour to finalize all the details. And now we have to go again.<br><br />
Lucky for us, modelers, computers dot care much about bacteria used in the experiment so as long as we follow the same pathway, we only need to rename variables. Bless!<br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math's, as Rachel and Kristin does some analytical derivations for our model's optimization. To be honest, we were very optimistic about the outcome, and though, the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack, even for MatLAB. <br><br />
<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done by Maciej.<br><br />
<br />
== Week 3 ==<br />
=== 16/07 ===<br />
Glasgow Bank Holiday.<br />
<br />
=== 17/07 ===<br />
We were given a brief introduction to Bionessie and SBML. Also we be begun to get to grips with Global Sensitivity analysis.<br />
<br />
=== 18/07 ===<br />
A brief overview of SimBiology was given to the drylab by Gary. Martina and Rachel continued learning about Stochastic modelling, while the rest of the team were working on Sensitivity Analysis.<br />
<br />
=== 19/07 ===<br />
A presentation was given to both, the wetlab and the drylab, about the Full Text Fetcher programme which, will help to search and retrive research articles.<br />
The Stochastic Simulation Algorithm (Gillespie's algorithm) is yet ready in the code to run some stochastics simulations on the Michaelis_Menten system.<br />
<br />
=== 20/07 ===<br />
Today we realized that, we missed few important details in our model 1. All morning was like one big mess. Everybody gave their ideas how things should be sorted. <br />
Eventually, we settled our brainstormed ideas on board and decided to leave simulations for Monday because new parameter hunt for model 1.2 was about to begin…<br />
Stochastic's work keeps on fitting the fano factor!<br />
<br />
== Week 4 ==<br />
=== 23/07 ===<br />
Day spent on long discussions with Raya about the accuracy of our model 1.2 . We finally simulated it and… Results were a bit, shall I say, unpleasant. Because of signal degradation, we will not reach a stable state as we anticipated before. That is going to mess up our optimization algorithms, for sure.<br />
<br />
=== 24/07 ===<br />
Kristin was asked by Xu to introduce Petri Net([http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html Snoopy]) method to qualitatively analyse the dynamics of the system. And Karolis, introduced a dynamical approach in modeling of the system using Simulink. Both methods rely not only on blunt programming, but introduce GUI (Graphical User Interface) logics. Respect the Stochastic Model, we are trying to run this one by doing some changes in the model (like changes in the signal, or other implementations).<br />
<br />
=== 25/07 ===<br />
Maciek started a thorough research of registry files, because we were told by dry lab, that they are about to deposit their first brick and, it is not very intuitive (a good point for registry’s future development). He promised to study it and give us all tutorial about his findings.<br />
<br />
=== 26/07 ===<br />
Bricks. Brick Bricks. What is this brick? What is the aim of having bricks? All these questions were brought forward and we all agreed to do a thorough individual research and combine them in joint brainstorm, because as our grandfathers used to say: ‘There are as many opinions, as there are heads’. Reachel and Martina continue working in cascade models for Stochastics.<br />
<br />
=== 27/07 ===<br />
First bricks from Glasgow team reached a sandpit. No no. Do not rush to copy them. That’s just a ‘getting used to the system’. We are about to deposit real one, so we want everything to go as smooth as possible.<br />
<br />
== Week 5 ==<br />
=== 30/07 ===<br />
Maciek’s tutorial enlightened wet and dry labs about all the registry’s pluses and minuses. We now know how to deposit a brick, edit it and etc. During this tutorial, we compiled a list of ides and suggestions, how to update the concept of brick itself, and some suggestions for registry’s future.<br />
<br />
=== 31/07 ===<br />
To pursue the further ideas about Brick-Based system modeling Karolis introduced some CAD techniqes for possible GUI algorithm and code development.<br />
<br />
=== 01/08 ===<br />
When the day was about to be over, we received long awaited news… First experimental data have finally reached us. We will be able to do some curve fitting, parameter estimation and other cool stuff?<br />
<br />
=== 02/08 ===<br />
Today we brainstormed the data we have. Everybody added their bit to ideas pot, however, since the data wasn’t that plentiful as we expected, we queried wet-lab for some more input. They promised, that more data is on the way.<br />
<br />
=== 03/08 ===<br />
Friday. The end of week 5. Our project just passed major milestone. No, not in development, but in time left available for us to complete it. We are, officially, halfway to successes now?<br />
<br />
== Week 6 ==<br />
=== 06/08 ===<br />
Today we received extra data to support our estimations. General modelers meting raised issues like the further development of the model, feedback loops, or our possible influence for wet lab. Now, that we have some data, (input) we should produce some output for near future projects.<br />
<br />
=== 07/08 ===<br />
Day was full of events. First thing in the morning, we had a modelers meeting, to discuss our final model’s layout. General structure and equations were drafted on board. From now we will be analyzing previous data from lab and try to simulate new model, called Model F1. <br><br />
Edinburgh team came to visit us after lunch. We exchanged some ideas about project, including modeling approaches and wet lab techniques used. After a brief introduction, we decided to continue our conversation outside the lab, so went to check what Glasgow could offer us.<br />
<br />
=== 08/008 ===<br />
Most of the day spent on Model F1, Model F1 Fedback and Model F1 Constitutive.<br />
<br />
=== 09/08 ===<br />
Even more types of models have been suggested to simulate. We have so much data now, so in order to manage it, we decided to document everything in LATEX. General standards are agreed for all the constants and equation. These are to be officially published later on.<br />
<br />
=== 10/08 ===<br />
Today we realized, that even almighty MATLAB, is not always the best solution. Since our experiments require LHS (Latin Hypercube Sampling) in huge numbers and Matlab does it in one hour. We decided to switch back to Good Old C++. Job well done and in 10 SECONDS ONLY???!!!! What has just happened knows only Maciek himself. Only he knows The Way Of Gods.<br />
<br />
== Week 7 ==<br />
=== 13/08 ===<br />
The day was quite productive, nerveless lucky. We manage to find 3 parameters of our interest. Besides that, we came with idea, how to compare qualitatively models F2 and F3 feedback. The method we developed and called ‘Feedback Logics’ allowed us to optimize four unknowns in F3 feedback. Results that came out suggested that addition of feedback loop for F3 will not influence the outcome of *** (sorry classified). Tomorrows meeting will decide, if F3 is wrong or it is the outcome one could expect.<br />
<br />
=== 14/08 ===<br />
?<br />
=== 15/008 ===<br />
?<br />
=== 16/08 ===<br />
?<br />
=== 17/08 ===<br />
?</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-14T11:12:08Z<p>Freestym: /* 24/07 */</p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We were introduced to the 'Nested Functions' to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menten equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab, explaining the methods we employ, as modellers, to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took us an hour to finalize all the details. And now we have to go again.<br><br />
Lucky for us, modelers, computers dot care much about bacteria used in the experiment so as long as we follow the same pathway, we only need to rename variables. Bless!<br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math's, as Rachel and Kristin does some analytical derivations for our model's optimization. To be honest, we were very optimistic about the outcome, and though, the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack, even for MatLAB. <br><br />
<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done by Maciej.<br><br />
<br />
== Week 3 ==<br />
=== 16/07 ===<br />
Glasgow Bank Holiday.<br />
<br />
=== 17/07 ===<br />
We were given a brief introduction to Bionessie and SBML. Also we be begun to get to grips with Global Sensitivity analysis.<br />
<br />
=== 18/07 ===<br />
A brief overview of SimBiology was given to the drylab by Gary. Martina and Rachel continued learning about Stochastic modelling, while the rest of the team were working on Sensitivity Analysis.<br />
<br />
=== 19/07 ===<br />
A presentation was given to both, the wetlab and the drylab, about the Full Text Fetcher programme which, will help to search and retrive research articles.<br />
The Stochastic Simulation Algorithm (Gillespie's algorithm) is yet ready in the code to run some stochastics simulations on the Michaelis_Menten system.<br />
<br />
=== 20/07 ===<br />
Today we realized that, we missed few important details in our model 1. All morning was like one big mess. Everybody gave their ideas how things should be sorted. <br />
Eventually, we settled our brainstormed ideas on board and decided to leave simulations for Monday because new parameter hunt for model 1.2 was about to begin…<br />
Stochastic's work keeps on fitting the fano factor!<br />
<br />
== Week 4 ==<br />
=== 23/07 ===<br />
Day spent on long discussions with Raya about the accuracy of our model 1.2 . We finally simulated it and… Results were a bit, shall I say, unpleasant. Because of signal degradation, we will not reach a stable state as we anticipated before. That is going to mess up our optimization algorithms, for sure.<br />
<br />
=== 24/07 ===<br />
Kristin was asked by Xu to introduce Petri Net([http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html Snoopy]) method to qualitatively analyse the dynamics of the system. And Karolis, introduced a dynamical approach in modeling of the system using Simulink. Both methods rely not only on blunt programming, but introduce GUI (Graphical User Interface) logics. Respect the Stochastic Model, we are trying to run this one by doing some changes in the model (like changes in the signal, or other implementations).<br />
<br />
=== 25/07 ===<br />
Maciek started a thorough research of registry files, because we were told by dry lab, that they are about to deposit their first brick and, it is not very intuitive (a good point for registry’s future development). He promised to study it and give us all tutorial about his findings.<br />
<br />
=== 26/07 ===<br />
Bricks. Brick Bricks. What is this brick? What is the aim of having bricks? All these questions were brought forward and we all agreed to do a thorough individual research and combine them in joint brainstorm, because as our grandfathers used to say: ‘There are as many opinions, as there are heads’.<br />
<br />
=== 27/07 ===<br />
First bricks from Glasgow team reached a sandpit. No no. Do not rush to copy them. That’s just a ‘getting used to the system’. We are about to deposit real one, so we want everything to go as smooth as possible.<br />
<br />
== Week 5 ==<br />
=== 30/07 ===<br />
Maciek’s tutorial enlightened wet and dry labs about all the registry’s pluses and minuses. We now know how to deposit a brick, edit it and etc. During this tutorial, we compiled a list of ides and suggestions, how to update the concept of brick itself, and some suggestions for registry’s future.<br />
<br />
=== 31/07 ===<br />
To pursue the further ideas about Brick-Based system modeling Karolis introduced some CAD techniqes for possible GUI algorithm and code development.<br />
<br />
=== 01/08 ===<br />
When the day was about to be over, we received long awaited news… First experimental data have finally reached us. We will be able to do some curve fitting, parameter estimation and other cool stuff?<br />
<br />
=== 02/08 ===<br />
Today we brainstormed the data we have. Everybody added their bit to ideas pot, however, since the data wasn’t that plentiful as we expected, we queried wet-lab for some more input. They promised, that more data is on the way.<br />
<br />
=== 03/08 ===<br />
Friday. The end of week 5. Our project just passed major milestone. No, not in development, but in time left available for us to complete it. We are, officially, halfway to successes now?<br />
<br />
== Week 6 ==<br />
=== 06/08 ===<br />
Today we received extra data to support our estimations. General modelers meting raised issues like the further development of the model, feedback loops, or our possible influence for wet lab. Now, that we have some data, (input) we should produce some output for near future projects.<br />
<br />
=== 07/08 ===<br />
Day was full of events. First thing in the morning, we had a modelers meeting, to discuss our final model’s layout. General structure and equations were drafted on board. From now we will be analyzing previous data from lab and try to simulate new model, called Model F1. <br><br />
Edinburgh team came to visit us after lunch. We exchanged some ideas about project, including modeling approaches and wet lab techniques used. After a brief introduction, we decided to continue our conversation outside the lab, so went to check what Glasgow could offer us.<br />
<br />
=== 08/008 ===<br />
Most of the day spent on Model F1, Model F1 Fedback and Model F1 Constitutive.<br />
<br />
=== 09/08 ===<br />
Even more types of models have been suggested to simulate. We have so much data now, so in order to manage it, we decided to document everything in LATEX. General standards are agreed for all the constants and equation. These are to be officially published later on.<br />
<br />
=== 10/08 ===<br />
Today we realized, that even almighty MATLAB, is not always the best solution. Since our experiments require LHS (Latin Hypercube Sampling) in huge numbers and Matlab does it in one hour. We decided to switch back to Good Old C++. Job well done and in 10 SECONDS ONLY???!!!! What has just happened knows only Maciek himself. Only he knows The Way Of Gods.<br />
<br />
== Week 7 ==<br />
=== 13/08 ===<br />
The day was quite productive, nerveless lucky. We manage to find 3 parameters of our interest. Besides that, we came with idea, how to compare qualitatively models F2 and F3 feedback. The method we developed and called ‘Feedback Logics’ allowed us to optimize four unknowns in F3 feedback. Results that came out suggested that addition of feedback loop for F3 will not influence the outcome of *** (sorry classified). Tomorrows meeting will decide, if F3 is wrong or it is the outcome one could expect.<br />
<br />
=== 14/08 ===<br />
?<br />
=== 15/008 ===<br />
?<br />
=== 16/08 ===<br />
?<br />
=== 17/08 ===<br />
?</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-14T11:11:39Z<p>Freestym: /* 24/07 */</p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We were introduced to the 'Nested Functions' to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menten equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab, explaining the methods we employ, as modellers, to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took us an hour to finalize all the details. And now we have to go again.<br><br />
Lucky for us, modelers, computers dot care much about bacteria used in the experiment so as long as we follow the same pathway, we only need to rename variables. Bless!<br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math's, as Rachel and Kristin does some analytical derivations for our model's optimization. To be honest, we were very optimistic about the outcome, and though, the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack, even for MatLAB. <br><br />
<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done by Maciej.<br><br />
<br />
== Week 3 ==<br />
=== 16/07 ===<br />
Glasgow Bank Holiday.<br />
<br />
=== 17/07 ===<br />
We were given a brief introduction to Bionessie and SBML. Also we be begun to get to grips with Global Sensitivity analysis.<br />
<br />
=== 18/07 ===<br />
A brief overview of SimBiology was given to the drylab by Gary. Martina and Rachel continued learning about Stochastic modelling, while the rest of the team were working on Sensitivity Analysis.<br />
<br />
=== 19/07 ===<br />
A presentation was given to both, the wetlab and the drylab, about the Full Text Fetcher programme which, will help to search and retrive research articles.<br />
The Stochastic Simulation Algorithm (Gillespie's algorithm) is yet ready in the code to run some stochastics simulations on the Michaelis_Menten system.<br />
<br />
=== 20/07 ===<br />
Today we realized that, we missed few important details in our model 1. All morning was like one big mess. Everybody gave their ideas how things should be sorted. <br />
Eventually, we settled our brainstormed ideas on board and decided to leave simulations for Monday because new parameter hunt for model 1.2 was about to begin…<br />
Stochastic's work keeps on fitting the fano factor!<br />
<br />
== Week 4 ==<br />
=== 23/07 ===<br />
Day spent on long discussions with Raya about the accuracy of our model 1.2 . We finally simulated it and… Results were a bit, shall I say, unpleasant. Because of signal degradation, we will not reach a stable state as we anticipated before. That is going to mess up our optimization algorithms, for sure.<br />
<br />
=== 24/07 ===<br />
Kristin was asked by Xu to introduce Petri Net([http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html Snoopy]) method to qualitatively analyse the dynamics of the system. And Karolis, introduced a dynamical approach in modeling of the system using Simulink. Both methods rely not only on blunt programming, but introduce GUI (Graphical User Interface) logics. Respect the Stochastic Model, we are trying to run this one by doing some changes in the model (like changes in the signal, or other implamantations).<br />
<br />
=== 25/07 ===<br />
Maciek started a thorough research of registry files, because we were told by dry lab, that they are about to deposit their first brick and, it is not very intuitive (a good point for registry’s future development). He promised to study it and give us all tutorial about his findings.<br />
<br />
=== 26/07 ===<br />
Bricks. Brick Bricks. What is this brick? What is the aim of having bricks? All these questions were brought forward and we all agreed to do a thorough individual research and combine them in joint brainstorm, because as our grandfathers used to say: ‘There are as many opinions, as there are heads’.<br />
<br />
=== 27/07 ===<br />
First bricks from Glasgow team reached a sandpit. No no. Do not rush to copy them. That’s just a ‘getting used to the system’. We are about to deposit real one, so we want everything to go as smooth as possible.<br />
<br />
== Week 5 ==<br />
=== 30/07 ===<br />
Maciek’s tutorial enlightened wet and dry labs about all the registry’s pluses and minuses. We now know how to deposit a brick, edit it and etc. During this tutorial, we compiled a list of ides and suggestions, how to update the concept of brick itself, and some suggestions for registry’s future.<br />
<br />
=== 31/07 ===<br />
To pursue the further ideas about Brick-Based system modeling Karolis introduced some CAD techniqes for possible GUI algorithm and code development.<br />
<br />
=== 01/08 ===<br />
When the day was about to be over, we received long awaited news… First experimental data have finally reached us. We will be able to do some curve fitting, parameter estimation and other cool stuff?<br />
<br />
=== 02/08 ===<br />
Today we brainstormed the data we have. Everybody added their bit to ideas pot, however, since the data wasn’t that plentiful as we expected, we queried wet-lab for some more input. They promised, that more data is on the way.<br />
<br />
=== 03/08 ===<br />
Friday. The end of week 5. Our project just passed major milestone. No, not in development, but in time left available for us to complete it. We are, officially, halfway to successes now?<br />
<br />
== Week 6 ==<br />
=== 06/08 ===<br />
Today we received extra data to support our estimations. General modelers meting raised issues like the further development of the model, feedback loops, or our possible influence for wet lab. Now, that we have some data, (input) we should produce some output for near future projects.<br />
<br />
=== 07/08 ===<br />
Day was full of events. First thing in the morning, we had a modelers meeting, to discuss our final model’s layout. General structure and equations were drafted on board. From now we will be analyzing previous data from lab and try to simulate new model, called Model F1. <br><br />
Edinburgh team came to visit us after lunch. We exchanged some ideas about project, including modeling approaches and wet lab techniques used. After a brief introduction, we decided to continue our conversation outside the lab, so went to check what Glasgow could offer us.<br />
<br />
=== 08/008 ===<br />
Most of the day spent on Model F1, Model F1 Fedback and Model F1 Constitutive.<br />
<br />
=== 09/08 ===<br />
Even more types of models have been suggested to simulate. We have so much data now, so in order to manage it, we decided to document everything in LATEX. General standards are agreed for all the constants and equation. These are to be officially published later on.<br />
<br />
=== 10/08 ===<br />
Today we realized, that even almighty MATLAB, is not always the best solution. Since our experiments require LHS (Latin Hypercube Sampling) in huge numbers and Matlab does it in one hour. We decided to switch back to Good Old C++. Job well done and in 10 SECONDS ONLY???!!!! What has just happened knows only Maciek himself. Only he knows The Way Of Gods.<br />
<br />
== Week 7 ==<br />
=== 13/08 ===<br />
The day was quite productive, nerveless lucky. We manage to find 3 parameters of our interest. Besides that, we came with idea, how to compare qualitatively models F2 and F3 feedback. The method we developed and called ‘Feedback Logics’ allowed us to optimize four unknowns in F3 feedback. Results that came out suggested that addition of feedback loop for F3 will not influence the outcome of *** (sorry classified). Tomorrows meeting will decide, if F3 is wrong or it is the outcome one could expect.<br />
<br />
=== 14/08 ===<br />
?<br />
=== 15/008 ===<br />
?<br />
=== 16/08 ===<br />
?<br />
=== 17/08 ===<br />
?</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-14T11:08:05Z<p>Freestym: /* 20/07 */</p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We were introduced to the 'Nested Functions' to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menten equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab, explaining the methods we employ, as modellers, to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took us an hour to finalize all the details. And now we have to go again.<br><br />
Lucky for us, modelers, computers dot care much about bacteria used in the experiment so as long as we follow the same pathway, we only need to rename variables. Bless!<br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math's, as Rachel and Kristin does some analytical derivations for our model's optimization. To be honest, we were very optimistic about the outcome, and though, the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack, even for MatLAB. <br><br />
<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done by Maciej.<br><br />
<br />
== Week 3 ==<br />
=== 16/07 ===<br />
Glasgow Bank Holiday.<br />
<br />
=== 17/07 ===<br />
We were given a brief introduction to Bionessie and SBML. Also we be begun to get to grips with Global Sensitivity analysis.<br />
<br />
=== 18/07 ===<br />
A brief overview of SimBiology was given to the drylab by Gary. Martina and Rachel continued learning about Stochastic modelling, while the rest of the team were working on Sensitivity Analysis.<br />
<br />
=== 19/07 ===<br />
A presentation was given to both, the wetlab and the drylab, about the Full Text Fetcher programme which, will help to search and retrive research articles.<br />
The Stochastic Simulation Algorithm (Gillespie's algorithm) is yet ready in the code to run some stochastics simulations on the Michaelis_Menten system.<br />
<br />
=== 20/07 ===<br />
Today we realized that, we missed few important details in our model 1. All morning was like one big mess. Everybody gave their ideas how things should be sorted. <br />
Eventually, we settled our brainstormed ideas on board and decided to leave simulations for Monday because new parameter hunt for model 1.2 was about to begin…<br />
Stochastic's work keeps on fitting the fano factor!<br />
<br />
== Week 4 ==<br />
=== 23/07 ===<br />
Day spent on long discussions with Raya about the accuracy of our model 1.2 . We finally simulated it and… Results were a bit, shall I say, unpleasant. Because of signal degradation, we will not reach a stable state as we anticipated before. That is going to mess up our optimization algorithms, for sure.<br />
<br />
=== 24/07 ===<br />
Kristin was asked by Xu to introduce Petri Net([http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html Snoopy]) method to qualitatively analyse the dynamics of the system. And Karolis, introduced a dynamical approach in modeling of the system using Simulink. Both methods rely not only on blunt programming, but introduce GUI (Graphical User Interface) logics.<br />
<br />
=== 25/07 ===<br />
Maciek started a thorough research of registry files, because we were told by dry lab, that they are about to deposit their first brick and, it is not very intuitive (a good point for registry’s future development). He promised to study it and give us all tutorial about his findings.<br />
<br />
=== 26/07 ===<br />
Bricks. Brick Bricks. What is this brick? What is the aim of having bricks? All these questions were brought forward and we all agreed to do a thorough individual research and combine them in joint brainstorm, because as our grandfathers used to say: ‘There are as many opinions, as there are heads’.<br />
<br />
=== 27/07 ===<br />
First bricks from Glasgow team reached a sandpit. No no. Do not rush to copy them. That’s just a ‘getting used to the system’. We are about to deposit real one, so we want everything to go as smooth as possible.<br />
<br />
== Week 5 ==<br />
=== 30/07 ===<br />
Maciek’s tutorial enlightened wet and dry labs about all the registry’s pluses and minuses. We now know how to deposit a brick, edit it and etc. During this tutorial, we compiled a list of ides and suggestions, how to update the concept of brick itself, and some suggestions for registry’s future.<br />
<br />
=== 31/07 ===<br />
To pursue the further ideas about Brick-Based system modeling Karolis introduced some CAD techniqes for possible GUI algorithm and code development.<br />
<br />
=== 01/08 ===<br />
When the day was about to be over, we received long awaited news… First experimental data have finally reached us. We will be able to do some curve fitting, parameter estimation and other cool stuff?<br />
<br />
=== 02/08 ===<br />
Today we brainstormed the data we have. Everybody added their bit to ideas pot, however, since the data wasn’t that plentiful as we expected, we queried wet-lab for some more input. They promised, that more data is on the way.<br />
<br />
=== 03/08 ===<br />
Friday. The end of week 5. Our project just passed major milestone. No, not in development, but in time left available for us to complete it. We are, officially, halfway to successes now?<br />
<br />
== Week 6 ==<br />
=== 06/08 ===<br />
Today we received extra data to support our estimations. General modelers meting raised issues like the further development of the model, feedback loops, or our possible influence for wet lab. Now, that we have some data, (input) we should produce some output for near future projects.<br />
<br />
=== 07/08 ===<br />
Day was full of events. First thing in the morning, we had a modelers meeting, to discuss our final model’s layout. General structure and equations were drafted on board. From now we will be analyzing previous data from lab and try to simulate new model, called Model F1. <br><br />
Edinburgh team came to visit us after lunch. We exchanged some ideas about project, including modeling approaches and wet lab techniques used. After a brief introduction, we decided to continue our conversation outside the lab, so went to check what Glasgow could offer us.<br />
<br />
=== 08/008 ===<br />
Most of the day spent on Model F1, Model F1 Fedback and Model F1 Constitutive.<br />
<br />
=== 09/08 ===<br />
Even more types of models have been suggested to simulate. We have so much data now, so in order to manage it, we decided to document everything in LATEX. General standards are agreed for all the constants and equation. These are to be officially published later on.<br />
<br />
=== 10/08 ===<br />
Today we realized, that even almighty MATLAB, is not always the best solution. Since our experiments require LHS (Latin Hypercube Sampling) in huge numbers and Matlab does it in one hour. We decided to switch back to Good Old C++. Job well done and in 10 SECONDS ONLY???!!!! What has just happened knows only Maciek himself. Only he knows The Way Of Gods.<br />
<br />
== Week 7 ==<br />
=== 13/08 ===<br />
The day was quite productive, nerveless lucky. We manage to find 3 parameters of our interest. Besides that, we came with idea, how to compare qualitatively models F2 and F3 feedback. The method we developed and called ‘Feedback Logics’ allowed us to optimize four unknowns in F3 feedback. Results that came out suggested that addition of feedback loop for F3 will not influence the outcome of *** (sorry classified). Tomorrows meeting will decide, if F3 is wrong or it is the outcome one could expect.<br />
<br />
=== 14/08 ===<br />
?<br />
=== 15/008 ===<br />
?<br />
=== 16/08 ===<br />
?<br />
=== 17/08 ===<br />
?</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-14T11:02:37Z<p>Freestym: /* 19/07 */</p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We were introduced to the 'Nested Functions' to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menten equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab, explaining the methods we employ, as modellers, to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took us an hour to finalize all the details. And now we have to go again.<br><br />
Lucky for us, modelers, computers dot care much about bacteria used in the experiment so as long as we follow the same pathway, we only need to rename variables. Bless!<br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math's, as Rachel and Kristin does some analytical derivations for our model's optimization. To be honest, we were very optimistic about the outcome, and though, the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack, even for MatLAB. <br><br />
<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done by Maciej.<br><br />
<br />
== Week 3 ==<br />
=== 16/07 ===<br />
Glasgow Bank Holiday.<br />
<br />
=== 17/07 ===<br />
We were given a brief introduction to Bionessie and SBML. Also we be begun to get to grips with Global Sensitivity analysis.<br />
<br />
=== 18/07 ===<br />
A brief overview of SimBiology was given to the drylab by Gary. Martina and Rachel continued learning about Stochastic modelling, while the rest of the team were working on Sensitivity Analysis.<br />
<br />
=== 19/07 ===<br />
A presentation was given to both, the wetlab and the drylab, about the Full Text Fetcher programme which, will help to search and retrive research articles.<br />
The Stochastic Simulation Algorithm (Gillespie's algorithm) is yet ready in the code to run some stochastics simulations on the Michaelis_Menten system.<br />
<br />
=== 20/07 ===<br />
Today we realized that, we missed few important details in our model 1. All morning was like one big mess. Everybody gave their ideas how things should be sorted. <br />
Eventually, we settled our brainstormed ideas on board and decided to leave simulations for Monday because new parameter hunt for model 1.2 was about to begin…<br />
<br />
== Week 4 ==<br />
=== 23/07 ===<br />
Day spent on long discussions with Raya about the accuracy of our model 1.2 . We finally simulated it and… Results were a bit, shall I say, unpleasant. Because of signal degradation, we will not reach a stable state as we anticipated before. That is going to mess up our optimization algorithms, for sure.<br />
<br />
=== 24/07 ===<br />
Kristin was asked by Xu to introduce Petri Net([http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html Snoopy]) method to qualitatively analyse the dynamics of the system. And Karolis, introduced a dynamical approach in modeling of the system using Simulink. Both methods rely not only on blunt programming, but introduce GUI (Graphical User Interface) logics.<br />
<br />
=== 25/07 ===<br />
Maciek started a thorough research of registry files, because we were told by dry lab, that they are about to deposit their first brick and, it is not very intuitive (a good point for registry’s future development). He promised to study it and give us all tutorial about his findings.<br />
<br />
=== 26/07 ===<br />
Bricks. Brick Bricks. What is this brick? What is the aim of having bricks? All these questions were brought forward and we all agreed to do a thorough individual research and combine them in joint brainstorm, because as our grandfathers used to say: ‘There are as many opinions, as there are heads’.<br />
<br />
=== 27/07 ===<br />
First bricks from Glasgow team reached a sandpit. No no. Do not rush to copy them. That’s just a ‘getting used to the system’. We are about to deposit real one, so we want everything to go as smooth as possible.<br />
<br />
== Week 5 ==<br />
=== 30/07 ===<br />
Maciek’s tutorial enlightened wet and dry labs about all the registry’s pluses and minuses. We now know how to deposit a brick, edit it and etc. During this tutorial, we compiled a list of ides and suggestions, how to update the concept of brick itself, and some suggestions for registry’s future.<br />
<br />
=== 31/07 ===<br />
To pursue the further ideas about Brick-Based system modeling Karolis introduced some CAD techniqes for possible GUI algorithm and code development.<br />
<br />
=== 01/08 ===<br />
When the day was about to be over, we received long awaited news… First experimental data have finally reached us. We will be able to do some curve fitting, parameter estimation and other cool stuff?<br />
<br />
=== 02/08 ===<br />
Today we brainstormed the data we have. Everybody added their bit to ideas pot, however, since the data wasn’t that plentiful as we expected, we queried wet-lab for some more input. They promised, that more data is on the way.<br />
<br />
=== 03/08 ===<br />
Friday. The end of week 5. Our project just passed major milestone. No, not in development, but in time left available for us to complete it. We are, officially, halfway to successes now?<br />
<br />
== Week 6 ==<br />
=== 06/08 ===<br />
Today we received extra data to support our estimations. General modelers meting raised issues like the further development of the model, feedback loops, or our possible influence for wet lab. Now, that we have some data, (input) we should produce some output for near future projects.<br />
<br />
=== 07/08 ===<br />
Day was full of events. First thing in the morning, we had a modelers meeting, to discuss our final model’s layout. General structure and equations were drafted on board. From now we will be analyzing previous data from lab and try to simulate new model, called Model F1. <br><br />
Edinburgh team came to visit us after lunch. We exchanged some ideas about project, including modeling approaches and wet lab techniques used. After a brief introduction, we decided to continue our conversation outside the lab, so went to check what Glasgow could offer us.<br />
<br />
=== 08/008 ===<br />
Most of the day spent on Model F1, Model F1 Fedback and Model F1 Constitutive.<br />
<br />
=== 09/08 ===<br />
Even more types of models have been suggested to simulate. We have so much data now, so in order to manage it, we decided to document everything in LATEX. General standards are agreed for all the constants and equation. These are to be officially published later on.<br />
<br />
=== 10/08 ===<br />
Today we realized, that even almighty MATLAB, is not always the best solution. Since our experiments require LHS (Latin Hypercube Sampling) in huge numbers and Matlab does it in one hour. We decided to switch back to Good Old C++. Job well done and in 10 SECONDS ONLY???!!!! What has just happened knows only Maciek himself. Only he knows The Way Of Gods.<br />
<br />
== Week 7 ==<br />
=== 13/08 ===<br />
The day was quite productive, nerveless lucky. We manage to find 3 parameters of our interest. Besides that, we came with idea, how to compare qualitatively models F2 and F3 feedback. The method we developed and called ‘Feedback Logics’ allowed us to optimize four unknowns in F3 feedback. Results that came out suggested that addition of feedback loop for F3 will not influence the outcome of *** (sorry classified). Tomorrows meeting will decide, if F3 is wrong or it is the outcome one could expect.<br />
<br />
=== 14/08 ===<br />
?<br />
=== 15/008 ===<br />
?<br />
=== 16/08 ===<br />
?<br />
=== 17/08 ===<br />
?</div>Freestymhttp://2007.igem.org/wiki/index.php/File:Modeling2.JPGFile:Modeling2.JPG2007-08-08T15:51:12Z<p>Freestym: </p>
<hr />
<div></div>Freestymhttp://2007.igem.org/wiki/index.php/User:FreestymUser:Freestym2007-07-26T05:54:37Z<p>Freestym: /* My name? MARTINA */</p>
<hr />
<div>[[Glasgow|Glasgow Main Page]]<br />
----<br />
===My name? MARTINA === <br />
<br />
[[Image:Martina.jpg|200px]]<br />
<br />
Hey!<br />
<br />
I’m a student of '''Statistics''' from Spain ('''''Barcelona''''', [http://www.uab.es/estudiants UAB]). I have just finished my degree at [http://www.gla.ac.uk University of Glasgow] and next year I’m going to do a Master by Research in Bioinformatics. My topics of interest are Time Series and Stochastic Modelling. <br />
<br />
But when I’m not at University... I’m a lover and addicted of ''sports'', I like to listen music, to play ''djembes'', to spend time in front of my laptop, and to lie in the sun. <br />
Can I recomend you a film?? -> [[Image:Pi1.jpg]]</div>Freestymhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-20T09:29:19Z<p>Freestym: </p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Mass-Action Reaction Modelling ==<br />
There are many advantages of modeling a biological system in differential equations. Predictions can be made for experiments before they are carried out in the wetlab which can prove to be very useful.<br />
<br />
The simplest reaction which is shown is simple decay where substance A decays to substance B. This can be modeled by two differential equations. The quantities which must be known to model these equations are the initial concentrations of both A and B and also the rate constant k1. By using Matlab a graph can be produced which shows that as A is used up B increases.<br />
<br />
[[Image:simpledecayequation.jpg|400px]]<br />
[[Image:simpledecay.jpg|400px]]<br />
<br />
<br />
The decay reaction can also take the form of becoming a reversible reaction where A turns into B via a rate constant of k1 while at the same time B turns into A via a rate constant of k2. This again is modeled by two differential equations<br />
<br />
[[Image:reversibleequation.jpg|400px]]<br />
[[Image:reversible.jpg|400px]]<br />
<br />
<br />
Another type of reaction which can be shown is an addition reaction where both A and B must be present to react to form C via a rate constant. Three differential equations are formed to model this reaction.<br />
<br />
[[Image:additionequation.jpg|400px]]<br />
[[Image:addition.jpg|400px]]<br />
<br />
An enzyme reaction can be modeled as shown below. The enzyme complex is modeled by using both the addition reaction and the reversible reaction. <br />
<br />
[[Image:enzymeequation.jpg|400px]]<br />
[[Image:enzyme.jpg|400px]]<br />
<br />
== RKIP network ==<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG | 700px]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
== Sensitivity ==<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in [[Mass-Action Reaction Modelling]] and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
== Michaelis-Menten ==<br />
''This was taken from 'Biochemistry' by 'Stryer'''<br><br />
''I apologise for the format of the equations i did not have them in a pdf document and the mathematical formula toolbox will not work''<br><br><br />
Anybody who has done any sort of biological study will know Michaelis-Menten what i am trying to acheive here is to take it from the basics so as to equate it to the equations we will be using to model the system and to give the biologists an idea of what values and models we need. In this case all k values are rate constants and [] means concentration and E is enzyme, S is substrate and [E]t is total enzyme concentration. <br><br />
The Michaelis-Menten equation describes the kinetic properties of many enzymes. Consider the simple system A -> P<br />
The rate of V is the quantity of A that disappears over a specified unit of time which is equal to the rate of appearance of P. For this system V=k[A] where k is the rate constant. <br />
The simplest model that accounts for the kinetic properties of many enzymes is (i will add it in when i have figured out how to)<br><br />
what we want is an expression that relates the rate of catalysis to the concentrations of substrate and enzyme and the rates of the individual steps.<br><br />
Our starting point is that the catalytic rate is equal to the product of the ES complex and k3.<br />
'''Vo=K2[ES]''' ''call this '''eqn(1)''' as i will be referring to it again''<br />
Now expressing [ES]in terms of known quantities the rates of '''formation''' and '''breakdown''' of [ES] are given by:<br />
'''formation [ES] = k1*[E]*[S]'''<br />
'''breakdown [ES] = (k2+k3)*[ES]'''<br />
A steady state occurs when the rates of formation and breakdown of the ES complex are equal, this gives the formula<br />
'''k1*[E]*[S]=(k2+k3)*[ES]'''<br />
which then gives <br />
'''[E][S] / [ES]=(k2+k3) / k1''' <br> <br />
This can be simplified by defining '''Km''' called the Michaelis constant<br><br />
'''Km = (k2+k3) / k1'''<br />
from this we get<br />
'''[ES] = [E][S] / Km''' ''call this '''eqn(2)''' as i will be referring to it again'' <br><br />
Now examining the numerator of this equation: because substrate is usually present at much higher concentrations than the enzyme, the concentration of uncombined substrate [S]is very nearly equal to the total substrate concentration. The concentration of enzyme [E] is equal to '''[E]t - [ES]''' now substituting this into ''eqn(2)'' and after some simplification we get<br />
'''[ES]=([E]t*[S]) / ([S]+Km)'''<br />
by substituting this expression into ''eqn(1)'' we get<br />
'''Vo = (k2[E]t*[S]) / ([s]+Km)'''<br />
The maximised rate Vmax is obtained when the catalytic sites on the enzyme are saturated with substrate i.e '''[ES] = [E]t''' thus<br />
'''Vmax = k2*[E]t<br />
this gives the Michaelis-Menten equation <br />
'''Vo = Vmax*([S] / ([S]+km)) ''' ''call this '''eqn(3)''' as i will refer to it again'' <br />
when '''[S]=Km''' then '''Vo = Vmax / 2'''. Thus Km is equal to the substrate concentration at which the reaction rate is half its maximal value.<br><br />
<br />
''The following part is from slides Raya showed us''<br><br />
Now relating this to gene transcription which we will be doing in this project. As any biologist will know<br><br />
'''Gene expression = production - degradation'''<br><br />
so '''μ’(t) = p(t) - δμ(t) ''' ''call this '''eqn(4)''' i will refer back to it''<br><br />
μ’(t) could be the production of mRNA for example.<br />
'''where P(t) = production rate and δ(t) = linear degredation rate''' <br><br />
We have the Michaeilis Menton model for the production (or transcription) rate. There is one for the '''activator''' and one for the '''repressor'''.<br><br />
'''Activator'''- The transcription factor '''TF''' ''increases'' the transcription rate of the gene:<br />
'''P(t)a =( β*[TF] / (γ + [TF]) ) + α''' ''call this '''eqn(5)'''''<br><br />
Where<br>β >0 is the maximum transcription rate which is equivalent to say '''Vmax''' in '''''eqn(3)'''''<br><br />
γ >0 is the half saturation constant which is equivalent to say '''Km''' in '''''eqn(3)'''''<br><br />
α >=0 is the basal rate of transcription (As far as i am aware this can be referred to as leakiness) which is taken into consideration to make the model more accurate.<br><br />
Now the equation for gene transcription for the '''activator''' is given by substituting '''''eqn(5)''''' into '''''eqn(4)''''' and assuming α=0.<br />
'''μ’(t)a = ( β*[TF] / (γ + [TF]) ) - δμ(t) '''<br><br />
'''Repressor''- The transcription factor '''TF''' ''decreases''the transcription rate of the gene:<br />
'''P(t)r =( β / (γ + [TF]) ) + α''' ''call this '''eqn(6)'''''<br><br />
Again the equation for gene transcription for the '''repressor''' is given by sunstituting '''''eqn(6)''''' into '''''eqn(5)''''' and assumingα=0. We get:<br />
'''μ’(t)r = ( β / (γ + [TF]) ) - δμ(t) '''<br> <br />
When considering more than one binding site we brinh '''h=number of binding sites into the equation''' so in both the '''activator''' and '''repressor''' equations for gene transcription '''whenever TF is in the equation you multiply it to the power of h'''.<br />
<br />
== Multiple Transcription Factors ==<br />
<br />
There is an extension of the formulas from Michaelis-Menten, for '''multiple transcription factors'''. <br />
<br />
''Regulation of gene expression is controlled by the binding of transcription factors to specific DNA sequences in gene promoter regions. Multiple transcription factor binding events are involved in the regulation of cellular processes.'' <br />
<br />
<br />
When we have more than one '''transcription factor''' (TF) involved we can find two situations:<br><br />
(In this page we will study the scenario with only 2 transcription factors involved) <br />
<br />
- SUM Gate.<br><br />
- ADD Gate.<br />
<br />
<br />
<u>'''SUM Gate'''</u>: As the word refers in this situation the effect from multiple TFs is additive. That means that the transcription could be induced for one '''OR''' other factor (or both together). But we have to note in this point that it’s not necessary the presence of both of them.<br />
<br />
<u>'''ADD Gate'''</u>: Implies the situation where the effect from multiple TFs is multiplicative. That means that the transcription will be induced for one '''AND''' the other factor at the same time (both actuate together). Nottice that if one of them is not active the transcription will not be done.<br />
<br />
<center>[[Image:formulas.jpg|400px]]</center><br />
== Modeling the behaviour in practice ==</div>Freestymhttp://2007.igem.org/wiki/index.php/Wet_to_DryWet to Dry2007-07-20T09:28:55Z<p>Freestym: </p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
This is an introduction for the dry lab into molecular and cellular biology. It will give an idea of the scientific techniques we use to manipulate DNA, and explain some of the words the dry lab may have already come across in their modeling.<br />
<br />
=== The Basics ===<br />
<br />
'''1.''' We are working with bacteria in our project. The membrane controls what is allowed in and out of the cell, and the nuclear material is a scrunched up ball of DNA called a chromosome.<br />
<br />
'''2.''' This is a human chromosome and it shows in more detail that a chromosome is a long strand of DNA compacted to take up as little space as possible inside a cell.<br />
<br />
'''3.''' This is what a strand of DNA looks like, and it can be referred to as a double helix. The long blue/green part is called the sugar phosphate backbone and the colored parts in the middle are called bases.<br />
<br />
'''4.''' This should give you an idea of what we mean by sugar phosphate backbone and bases. The left hand side of the picture shows how sugar phosphate units hold bases in place in DNA. The bases are the yellow shapes and each base corresponds to a letter: A, C, G, or T. These letters stand for the molecules shown on the right hand side of the picture (Uracil is used in RNA to replace Thymine).<br />
<br />
'''5.''' DNA replication. In DNA the double strand is made when the bases of two strands join to form base pairs. A always pairs with T, and C always pairs with G. When more copies of DNA are being made the double helix strand separates and new bases are brought in to make an identical copy of the original double strand.<br />
<br />
'''6.''' This picture goes into more detail than the dry lab needs to know, but is being used here to explain DNA polymerase. When DNA replicates the double strand splits and an enzyme called DNA polymerase moves along the strand bringing in new bases to make the single strand a double strand.<br />
<br />
'''7.''' The DNA polymerase knows where to start because a primer marks the start point. In this picture the primer is shown in green. Primers will be explained in more detail later.<br />
<br />
'''8.''' Making Proteins. Living things are made up of proteins, loads and loads of different proteins. A protein is a really long molecule made up of smaller molecules which act as building blocks called amino acids. Amino acids in a long chain will react with other amino acids in the same chain causing the long molecule to fold into a shape (quaternary protein structure). A sequence of DNA which makes a full protein is called a gene.<br />
<br />
'''9.''' There are 20 amino acids altogether, and here they are.<br />
<br />
'''10.''' DNA is a valuable resource to a cell because it provides the code for making all of the proteins the cell will ever need. For this reason, when a protein is being made the cell uses a sort of back up copy of the code called RNA. In RNA U always pairs with A, because U replaces T. This picture shows how this RNA is made in a process called transcription. An enzyme called RNA polymerase moves along a double strand of DNA, separates it and brings in bases which pair to the single strand. This results in a newly made strand of RNA.<br />
<br />
'''11.''' After transcription comes translation where the RNA is read and a translated into a protein. The RNA can be separated into codons which are groups of 3 bases. Each codon corresponds to an amino acid.<br />
<br />
'''12.''' The Table of Codons shows every possible combination of bases in a 3 base codon and which amino acid it translates into.<br />
<br />
'''13.''' Every cell contains ribosomes. Ribosomes translate RNA into amino acids. In RNA the codon AUG signals to the ribosome to start translation, and UAA, UAG and UGA signal to stop. This picture is slightly more detailed than it needs to be but shows a ribosome reading along RNA and translating it into a string of amino acids.<br />
<br />
'''14.''' An overall view of transcription and translation. RNA polymerase binds to DNA and transcibes it into RNA. RNA (red) is read by ribosomes and translated into proteins.<br />
<br />
'''15.''' So how is the RNA polymerase meant to know where on the DNA it has to start transcribing? Several base pairs before the RNA polymerase binding site is a sequence of bases called a promoter. Proteins called transcription factors recognise this promoter sequence and bind to it. This signals to RNA polymerase to come and bind as well so that it can start transcription.<br />
<br />
=== Restriction Enzymes ===<br />
<br />
'''1.''' A restriction enzyme is a protein that can cut DNA. There are many different restriction enzymes, and each one recognises a different sequence in DNA which it will then cut. The sequence is the same when it is read 5' to 3' on each strand, as seen in the the picture.<br />
<br />
'''2.''' Each restriction enzyme leaves its own cutting mark referred to as a sticky end.<br />
<br />
'''3.''' Two pieces of DNA with the same sticky ends can be glued (ligated) together with an enzyme called ligase.<br />
<br />
<u>Example</u> <br><br />
Say there are two pieces of DNA, A and B. A contains a gene of interest, and B is a plasmid (a plasmid is a complete circle of DNA found in bacteria separate from the chromosome which can be taken out of one cell and put into another). In piece A there is a restriction site before the gene of interest and another after the gene of interest which are both recognised and cut by a restriction enzyme called XbaI. In the plasmid B there is another restriction site recognised and cut by XbaI. The gene of interest can be cut out and pasted into the restriction site of the plasmid.<br />
<br />
=== Primers ===<br />
<br />
'''1.''' Primers are short pieces (about 20 nucleotides) of RNA or DNA that bind specifically to their complementary DNA sequence in a certain Tm temperature according to their GC-% content.<br />
<br />
'''2.''' Primers able the DNA polymerase enzyme to add free nucleotides to the growing 3’ end of the primer. Every added nucleotide is chosen so that G pairs with C and A with T thus resulting in a new complementary strand.<br />
<br />
'''3.''' It is possible to introduce specific changes into the DNA sequence by using “mutated” primers that have carefully chosen and changed bases in their sequence. This technique is called Site Directed Mutagenesis and it can be used for getting rid of unwanted restriction sites in the middle of an important gene sequence for example.<br />
<br />
'''4.''' Primers need to be carefully designed to make sure they bind only to the target sequence and not to each others for example. They are then ordered commercially.<br />
<br />
<u>Example</u> <br><br />
A well designed primer could look like this: 5´CGTCCAGTACGCGATGCTAGAC3´<br />
<br />
=== PCR (Polymerase Chain Reaction) ===<br />
<br />
'''1.''' A polymerase chain reaction amplifies a known sequence of the DNA genome with the help of primers and DNA polymerase enzyme.<br />
<br />
'''2.''' Primers bind to the template DNA on each sides of our gene of interest. DNA polymerase copies the template strand during the extension step of the PCR cycle.<br />
<br />
'''3.''' The actual PCR program takes place in a thermo cycler that cycles through three different temperatures; separating the DNA strands, annealing the primers and extending the primers.<br />
<br />
'''4.''' PCR is extremely sensitive and can amplify millions of copies of DNA from just only few follicle cells surrounding a single pulled-out hair for example.<br />
<br />
=== Transformation ===<br />
<br />
'''1.''' During the transformation the plasmid DNA is put into the antibiotic-sensitive bacterial cells. <br />
<br />
'''2.''' To get started bacterial cell wall and plasma membrane has to be made permeable and the chosen DNA plasmid is taken up by the cell during the heat shock.<br />
<br />
'''3.''' Antibiotic selection makes it easy to see which bacterial cells have taken up the plasmid DNA and thus a resistance gene for an antiobiotic. An antibiotic resistance gene makes the cells able to live in a plate containing antibiotics.<br />
<br />
Check out the PowerPoint slides to see pictures!<br />
<br />
[[Media:Lecture from Wetlab to Drylab.ppt]]</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/LecturesGlasgow/Lectures2007-07-20T09:28:43Z<p>Freestym: </p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
The aim of these informal lectures was to give each side of the team an insight into the other as we are not 'modellers' and 'biologists' we are a team. The dry lab people also had a day of working in the lab with Emma and were promised that their experiments were going to be used in the project (that was possibly just to make us feel better though).<br><br />
<br />
[[Wet to Dry | '''Lecture given by Wetlab to Drylab''']]<br><br />
[[Dry to Wet | '''Lecture given by Drylab to Wetlab''']]</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/WetlabGlasgow/Wetlab2007-07-20T09:28:19Z<p>Freestym: </p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
{|cellspacing="6px" cellpadding="16" border="0" width="100%"<br />
|-<br />
|[[Glasgow/Wetlab/Protocols|PROTOCOLS]]<br />
|[[Glasgow/Wetlab/References|REFERENCES]]<br />
|[[Glasgow/Wetlab/Orders|ORDERS]]<br />
|}<br />
== Week 1 ==<br />
=== 03/07 ===<br />
#Maija and Christine prepared LB broth and LB agar with [[Glasgow/Wetlab/Protocols|Protocol 1]]. Made 4 batches of plates, 2 with kanamycin and 2 with carbenicillin.<br />
<br />
=== 04/07 ===<br />
#All wetlab researched BioBricks.<br />
#Reporter constructs and mini-Tn5 stocks looked out.<br />
#Streaked the following:<br />
#*P. putida PAW 340 pJAK14 (Carb. plate)<br />
#*Tn5 lux AB (Carb. plate)<br />
#*Mini-Tn5 lux AB (Carb. plate)<br />
#*P. Fluorescens NCIMB 9815 (Carb. plate)<br />
#*P. putida KT2440 (LB)<br />
#*JM109 pBluescript 5k+ (Carb. plate)<br />
#*Mini-Tn5 Tc (Carb. Plate)<br />
#*pQF52 (Carb. plate)<br />
#*P. Fluorescens 9815 (LB)<br />
#*E. coli pJAK14 (Km plate)<br />
#*Il DntR in pOF52 (Carb. plate)<br />
#*pUCINR in Ω strain C (Carb. plate)<br />
#*pGLTUR (Carb. plate)<br />
#*Mini-Tn5 Kan (Carb. plate)<br />
#*Mini-Tn5 Sm/Sp (Carb. plate)<br />
#*Mini-Tn5 1cc2 (Carb. plate)<br />
#*E. coli Sa1 (LB)<br />
#*DmpR #24 (Carb. plate)<br />
#*Mini-Tn5 lac 32 in E. coli 517 (Carb. plate)<br />
#*Mini-Tn5 Tc (Carb. Plate)<br />
#*Mini-Tn5 Cm (Carb. plate)<br />
#*DmpR WT (Carb. plate)<br />
#*E.coli sm 10 pESD15 Tn5 GFP (Carb. plate)<br />
#*pUJ8 (Carb. Plate)<br />
<br />
=== 05/07 ===<br />
#BioBricks – Maija and Scott transformed using [[Glasgow/Wetlab/Protocols | Protocol 2]]<br />
#*BBa_p1010 (DB3.1) (death gene plasmid) Plate 4: 7A – p5B1A10, 11E – p5B1A10 and 11C – p5B3K3<br />
#*BBa_IS2001 (Top10) (high copy number plasmid) Plate 4: 5I – p5B4A5, 5D – p5B4K5, 6B – p5B3K5, 6D – p5B4K5 and 6E – p5B4A5 (Also 5K, 5M, 4J, 4L, 4N, 4P)<br />
#*BBa_J23119 (Top 10) (strong constitutive promoter) Plate 3: 19A – pB1A2 (V1013)<br />
#*BBa_R0062 (Top 10) (HSL and luxR inducible) Plate 1: 9G – pSB1A2 (V1004)<br />
#*BBa_J04500 (Top 10) (IPTG inducible prom + RBS) Plate 1: 16P – p5B1AK3 (V1009)<br />
#*BBa_E0040 (Top 10) (GFP mutant no promoter (3b)) Plate 1: 5H – p5B1A2 (V1001)<br />
#Maia and Christine researched restriction enzymes for the reporter constructs and Mini-Tn5s streaked on 4/7/07 and digested some. Had planned to make biobricks using Mini-Tn5s etc but discovered that a previous attempt to use transposable elements to make biobricks had been unsuccessful due to scarring at the restriction site. http://partsregistry.org/Part:BBa_J61206<br />
<br />
=== 06/07 ===<br />
#Maija and Christine made 10x stocks for M9 (see [[Glasgow/Wetlab/Protocol|Protocol 3]]).<br />
#Tutorial in BioEdit and Primer3.<br />
#Started designing primers for amplification and site directed mutagenesis of DmpR and DmpR #24 (see [[Glasgow/Wetlab/Protocols | Protocol 4]]).<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
#Christine and Maija designed primers for site directed mutagenesis in DmpR, DmpR #24, ****, **** and ****, and amplification of DmpR and DmpR #24. Used [[Glasgow/Wetlab/Protocols|Protocol 4]], and to check Tm http://www.itt-biotech.de/itt-cgi/oligo-tm.pl<br />
#Mai carried out restriction digests of DmpR and DmpR #24. Results were poor and gel gave poor visibility.<br />
#Scott retransformed any of the transformations that did not work from the transformations from 5/7/07.<br />
#*4/11C BBa_p1010 pSB3K3 death gene<br />
#*4/5I BBa_I522001 pSB4A5 hi-copy<br />
#*4/5D BBa_I522001 pSB4K5 hi-copy<br />
#*4/6B BBa_I522001 pSB3K3 hi-copy<br />
#*4/6D BBa_I522001 pSB4K hi-copy<br />
#*1/5H BBa_E0040 pSB1A2 GFP non promoter<br />
#Used transformations that did work and set them up tubes of LB for minipreps tomorrow.<br />
#*BBa_I52001 death gene plasmid (hi copy number)<br />
#*BBa-J23119 strong constitutive promoter<br />
#*BBa_R0062 HSL and luxR inducible<br />
#*BBa_306500 IPTG inducible and RBS<br />
Plan is to use DmpR and DmpR #24 to detect phenol and produce lacZ. Grown on Xgal the better the bacteria detect phenol, the more blue they will be in a spectrophotometer.<br />
<br />
=== 10/07 ===<br />
#Mai did minipreps, according to Qiagen prepkit manual (see [[Glasgow/Wetlab/Protocols|Protocol 5]]), of the transformations grown in LB last night (9/7/07).<br />
#Wetlab and Drylab gave presentations to the team to explain key terms used in the lab (see [[Wet to Dry|Tutorials]]).<br />
#Christine made tetracycline stock – 250 mg tetracycline in 50ml 100% ethanol to make 5mg/ml stock.<br />
#Maija made thiamine stock (0.8g thiamine in 20ml dH2O and filter sterilized. Kept in freezer in foil (light sensitive).<br />
#Christine grew E. coli pJAK14 in LB overnight at 37°C following protocol from Wise et al, 2000).<br />
#Scott and Lynsey grew DmpR and DmpR #24 overnight in LB with Tc and Carb. This is because the plates streaked on 4/7/07 for DmpR and DmpR #24 did not grow, and restriction digests on 9/7/07 used up most of the DNA. What is grown will be mini-prepped and restriction digested tomorrow.<br />
#*2x 5ml LB containing carb (50ug/ml) with DmpR<br />
#*2x 5ml LB containing carb (50ug/ml) with DmpR #24<br />
#*2x 5ml LB containing Tc (50ug/ml) with DmpR<br />
#*2x 5ml LB containing Tc (50ug/ml) with DmpR #24<br />
#*2x 5ml LB containing Tc (10ug/ml) with DmpR<br />
#*2x 5ml LB containing Tc (10ug/ml) with DmpR #24<br />
#Scott's retransformations (9/7/07) all worked (esp Top 10s, not so much DB3.1). To be mini-prepped tomorrow.<br />
<br />
=== 11/07 ===<br />
#Lynsey mini-prepped Scott's retransformed biobricks (9/7/07) according to Qiagen Prepkit Manual.<br />
#Maija prepared glycerol for freezing the transformations in LB.<br />
#Can not mini-prep DmpR or DmpR #24 in Tc because it did not grow well overnight. Time for Plan B.<br />
#*'''Plan B'''<br>DmpR is not working – not growing or digesting as we would expect it to. Instead of DmpR we will try XylR which detects BETX compounds (benzene, toluene, and xylene) and DntR which detects salictlate and could be modified to detect TNT and DNT. For this we will be using pGLTUR and pQF52.<br />
#We all began to design primers for site directed mutagenesis (SDM) and amplification of XylR, Pr, Pu and DntR.<br />
<br />
=== 12/07 ===<br />
<u>XylR, Pr, and Pu</u><br />
#Searched [http://www.ncbi.nlm.nih.gov/Genbank GenBank] for pWW0 which contains XylR, Pr and Pu. Saved in BioEdit.<br />
#Using the XylR sequence (Inouye et al, 1988) we were able to design primers for the amplification of XylR.<br />
#Using previously designed primers (Willardson et al, 1998) we were able to locate the beginning of Pr and designed primers to amplify the sequence between the beginning of Pr and the beginning of XylR.<br />
#From previously designed primers (Willardson et al, 1998) we were able to locate a sequence we believed to be Pu and designed primers. To be sure we also searched pWW0 sequence with Primer3 to locate on the plasmid where the Willardson Pu primers would attach. Using BioEdit we located another sequence we also suspect to be Pu. We now have primers designed for both suspected sequences.<br />
#Also designed primers for site directed mutagenesis of the PstI site in XylR.<br />
(We were unable to use the Willardson primers for our purposes because they were designed to contain restriction sites, instead we used them to locate the genes of interest).<br />
<br />
<u>DntR</u><br />
#Scott found an article containing the sequence for DntA and some of DntR, then we used BlastX to find the sequence of DntR. From this we were able to design primers to amplify the sequence.<br />
#Also designed primers so we can sequence pQF52 because the lacZ gene is not complete in the plasmid and we need to know its sequence.<br />
<br />
=== 13/07 ===<br />
#Began typing up protocols for the Wiki.<br />
#Ordered primers, made changes to DntR_suffix_1 which will arrive later. (See Orders)<br />
#Wiki meeting. Maija, Christine H, Majeik, Toby, Christine M, Mai, Scott and Lynsey.</div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/Meet_the_teamGlasgow/Meet the team2007-07-20T09:27:53Z<p>Freestym: </p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
<center>[[Image:Glasgow team photo.jpg|600px]]<br><br />
Glasgow iGEM 2007 Team</center><br />
__NOTOC__<br />
<br />
== Team Members ==<br />
<br />
=== Students ===<br />
{| cellspacing="6px" cellpadding="16" border="0" width="100%"<br />
|-<br />
|style="background:#CCFFFF" | <center>[[Image:TobyF.jpg|190px]]<br> [[User:toby|Toby Friend]] [[Image:Glasgow_flags_en.png|England]]</center><br />
|style="background:#CCFFFF" | <center>[[Image:RachaelF.jpg|190px]] <br> [[User:Rach|Rachael Fulton]] [[Image:Glasgow_flags_sc.png|Scotland]]</center><br />
|style="background:#CCFFFF" | <center> [[Image:ChristineH.jpg|190px]] <br> [[User:charkness|Christine Harkness]] </center><br />
|style="background:#CCFFFF" | <center>[[Image:Maia-BrittJ.jpg|190px]] <br> [[User:mojs|Mai-Britt Jensen]] [[Image:Glasgow_flags_dk.png|Denmark]] </center><br />
|-<br />
|style="background:#CCFFFF" | <center>[[Image:KarolisK.jpg|190px]] [[User:0602359k |Karolis Kidykas]] [[Image:Glasgow_flags_lt.png|Lithuania]]</center><br />
|style="background:#CCFFFF" | <center>[[Image:MartinaM.jpg|190px]] [[User:freestym|Martina Marbà]] [[Image:Glasgow_flag_es.png|Spain]]</center><br />
|style="background:#CCFFFF" | <center>[[Image:LynseyM.jpg|190px]] [[User:L.McLeay|Lynsey McLeay]] [[Image:Glasgow_flags_en.png|England]]</center><br />
|style="background:#CCFFFF" | <center>[[Image:ChristineM.jpg|190px]] [[User:christinemerrick|Christine Merrick]] [[Image:Glasgow_flags_sc.png|Scotland]]</center><br />
|-<br />
|style="background:#CCFFFF" | <center>[[Image:MaijaEP.jpg|190px]] [[User:MaijaP|Maija Paakkunainen]] [[Image:Glasgow_flags_fi.png|Finland]]</center><br />
|style="background:#CCFFFF" | <center>[[Image:ScottR.jpg|190px]] [[User:scott.w.ramsay|Scott Ramsay]] [[Image:Glasgow_flags_sc.png|Scotland]]</center><br />
|style="background:#CCFFFF" | <center>[[Image:MaciejT.jpg|190px]] [[User:mcek|Maciej Trybiło]] [[Image:Glasgow_flags_pl.png|Poland]]</center><br />
|}<br />
<br />
=== Instructors === <br />
[[User:dforehand|David Forehand]]<br><br />
<!--[[User:DavidGilbert|David Gilbert]]<br> --><br />
[http://www.brc.dcs.gla.ac.uk/~drg David Gilbert]<br><br />
[[User:GaryGray|Gary Gray]]<br><br />
[[User:gux|Xu Gu]] [[Image:Glasgow_flags_cn.png|China]]<br><br />
[[User:ghamilton1|Graham Hamilton]]<br><br />
[[User:raya|Raya Khanin]] <br> <!-- Raya must register --><br />
[[User:corriecas|David Leader]]<br><br />
[[User:Susanrosser|Susan Rosser]]<br><br />
[[User:EmmaTravis|Emma Travis]]<br><br />
<br />
<br />
== Diary ==<br />
{| cellspacing="2px" cellpadding="20" border="0" width="100%"<br />
|-<br />
|<center>[[Image:Week 2.jpg]] <br> '''[[Glasgow/Meet the team/Week1|Week 1]]''' </center><br />
|<center>[[Image:Week 1.JPG]] <br> '''[[Glasgow/Meet the team/Week2|Week 2]]''' </center><br />
|<center>[[Image:Week 3.JPG]] <br> '''[[Glasgow/Meet the team/Week3|Week 3]]''' </center><br />
|<center>[[Image: Glasgow_picoftheweek.gif]] <br> '''[[Glasgow/Meet the team/Week4|Week 4]]''' <br> Incoming!</center><br />
|<center>[[Image: Glasgow_picoftheweek.gif]] <br> '''[[Glasgow/Meet the team/Week5|Week 5]]''' <br> Incoming!</center><br />
|-<br />
|<center>[[Image: Glasgow_picoftheweek.gif]] <br> '''[[Glasgow/Meet the team/Week6|Week 6]]''' <br> Incoming!</center><br />
|<center>[[Image: Glasgow_picoftheweek.gif]] <br> '''[[Glasgow/Meet the team/Week7|Week 7]]''' <br> Incoming!</center><br />
|<center>[[Image: Glasgow_picoftheweek.gif]] <br> '''[[Glasgow/Meet the team/Week8|Week 8]]''' <br> Incoming!</center><br />
|<center>[[Image: Glasgow_picoftheweek.gif]] <br> '''[[Glasgow/Meet the team/Week9|Week 9]]''' <br> Incoming!</center><br />
|<center>[[Image: Glasgow_picoftheweek.gif]] <br> '''[[Glasgow/Meet the team/Week10|Week 10]]''' <br> Incoming!</center><br />
|}</nowiki></div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-07-20T09:08:14Z<p>Freestym: </p>
<hr />
<div><u>[[Glasgow|Glasgow Main Page]]</u><br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We are were introduced to the Nested function to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menton equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab explaining the methods we employ as modellers to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
[[User:Toby|Toby]] 11:27, 11 July 2007 (EDT)<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took me an hour to finalize all the details. And now I have to go again.<br><br />
Lucky for us modelers, computers dot care much about bacteria used in experiment so as long as we follow the same path we only need to rename variables. Bless! <br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math as Rachel and Kristin does some analytical derivations for our models optimization. To be honest, we were very optimistic about the outcome, and though the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack even for MatLAB. <br><br />
<br />
--[[User:0602359k|Karolis]] 04:53, 13 July 2007 (EDT)<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done it by Maciej.<br></div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-07-20T08:51:25Z<p>Freestym: </p>
<hr />
<div>[[Glasgow|Glasgow Main Page]]<br />
<br />
== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We are were introduced to the Nested function to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menton equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab explaining the methods we employ as modellers to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
[[User:Toby|Toby]] 11:27, 11 July 2007 (EDT)<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took me an hour to finalize all the details. And now I have to go again.<br><br />
Lucky for us modelers, computers dot care much about bacteria used in experiment so as long as we follow the same path we only need to rename variables. Bless! <br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math as Rachel and Kristin does some analytical derivations for our models optimization. To be honest, we were very optimistic about the outcome, and though the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack even for MatLAB. <br><br />
<br />
--[[User:0602359k|Karolis]] 04:53, 13 July 2007 (EDT)<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done it by Maciej.<br></div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-07-20T08:34:23Z<p>Freestym: /* 13/07 */</p>
<hr />
<div>== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We are were introduced to the Nested function to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menton equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab explaining the methods we employ as modellers to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
[[User:Toby|Toby]] 11:27, 11 July 2007 (EDT)<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took me an hour to finalize all the details. And now I have to go again.<br><br />
Lucky for us modelers, computers dot care much about bacteria used in experiment so as long as we follow the same path we only need to rename variables. Bless! <br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math as Rachel and Kristin does some analytical derivations for our models optimization. To be honest, we were very optimistic about the outcome, and though the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack even for MatLAB. <br><br />
<br />
--[[User:0602359k|Karolis]] 04:53, 13 July 2007 (EDT)<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done it by Maciej.<br></div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-07-20T08:32:30Z<p>Freestym: /* 12/07 */</p>
<hr />
<div>== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We are were introduced to the Nested function to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menton equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab explaining the methods we employ as modellers to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
[[User:Toby|Toby]] 11:27, 11 July 2007 (EDT)<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took me an hour to finalize all the details. And now I have to go again.<br><br />
Lucky for us modelers, computers dot care much about bacteria used in experiment so as long as we follow the same path we only need to rename variables. Bless! <br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math as Rachel and Kristin does some analytical derivations for our models optimization. To be honest, we were very optimistic about the outcome, and though the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack even for MatLAB. <br><br />
<br />
--[[User:0602359k|Karolis]] 04:53, 13 July 2007 (EDT)<br />
=== 13/07 ===<br />
Some introduction to Stochastic Modelling intrinsicaly contained in gene transcription. We took some decisions about the design of the wiki. More optimization done it by Macieck.<br></div>Freestymhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-07-20T08:25:29Z<p>Freestym: </p>
<hr />
<div>== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We are were introduced to the Nested function to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menton equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab explaining the methods we employ as modellers to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
[[User:Toby|Toby]] 11:27, 11 July 2007 (EDT)<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took me an hour to finalize all the details. And now I have to go again.<br><br />
Lucky for us modelers, computers dot care much about bacteria used in experiment so as long as we follow the same path we only need to rename variables. Bless! <br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math as Rachel and Kristin does some analytical derivations for our models optimization. To be honest, we were very optimistic about the outcome, and though the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack even for MatLAB. <br><br />
<br />
--[[User:0602359k|Karolis]] 04:53, 13 July 2007 (EDT)<br />
=== 12/07 ===<br />
A day dedicated to manual math as Rachel and Kristin does some analytical derivations for our models optimization. To be honest, we were very optimistic about the outcome, and though the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack even for MatLAB. <br></div>Freestymhttp://2007.igem.org/wiki/index.php/User:FreestymUser:Freestym2007-07-20T01:50:57Z<p>Freestym: </p>
<hr />
<div>===My name? MARTINA === <br />
<br />
[[Image:Martina.jpg|200px]]<br />
<br />
Hey!<br />
<br />
I’m a student of '''Statistics''' from Spain ('''''Barcelona''''', [http://www.uab.es/estudiants UAB]). I have just finished my degree at [http://www.gla.ac.uk University of Glasgow] and next year I’m going to do a Master by Research in Bioinformatics. My topics of interest are Time Series and Stochastic Modelling. <br />
<br />
But when I’m not at University... I’m a lover and addict of ''sports'', I like to listen music, to play ''djembes'', to spend time in front of my laptop, and to lie in the sun. <br />
Can I recomend you a film?? -> [[Image:Pi1.jpg]]</div>Freestymhttp://2007.igem.org/wiki/index.php/User:FreestymUser:Freestym2007-07-20T01:42:42Z<p>Freestym: </p>
<hr />
<div>===My name? MARTINA === <br />
<br />
[[Image:Martina.jpg|200px]]<br />
<br />
Hey!<br />
<br />
I’m a student of '''Statistics''' from Spain ('''''Barcelona''''', [http://www.uab.es/estudiants UAB]). I have just finished my degree at [http://www.gla.ac.uk University of Glasgow] and next year I’m going to do a Master by Research in Bioinformatics. My topics of interest are Time Series and Stochastic Modelling. <br />
<br />
But when I’m not at University... I’m a lover and addict of ''sports'', I like to listen music, to play ''djembes'', to spend time in front my laptop, and to lie in the sun. <br />
Can I recomend you a film?? -> [[Image:Pi1.jpg]]</div>Freestymhttp://2007.igem.org/wiki/index.php/User:FreestymUser:Freestym2007-07-20T01:38:07Z<p>Freestym: </p>
<hr />
<div>--My name? MARTINA--<br />
<br />
[[Image:Martina.jpg|200px]]<br />
<br />
Hey!<br />
<br />
I’m a student of '''Statistics''' from Spain ('''''Barcelona''''', [http://www.uab.es/estudiants UAB]). I have just finished my degree at [http://www.gla.ac.uk University of Glasgow] and next year I’m going to do a Master by Research in Bioinformatics. My topics of interest are Time Series and Stochastic Modelling. <br />
<br />
But when I’m not at University... I’m a lover and addict of ''sports'', I like to listen music, to play ''djembes'', to spend time in front my laptop, and to lie in the sun. <br />
Can I recomend you a film?? -> [[Image:Pi1.jpg]]</div>Freestymhttp://2007.igem.org/wiki/index.php/File:Martina.jpgFile:Martina.jpg2007-07-20T01:26:22Z<p>Freestym: </p>
<hr />
<div></div>Freestymhttp://2007.igem.org/wiki/index.php/User:FreestymUser:Freestym2007-07-20T01:25:35Z<p>Freestym: </p>
<hr />
<div>[[Image:Martina.jpg|200px]]<br />
<br />
Hey!<br />
<br />
I’m a student of '''Statistics''' from Spain ('''''Barcelona''''', UAB). I have just finished my degree at University of Glasgow and next year I’m going to do a Master by Research in Bioinformatics. My topics of interest are Time Series and Stochastic Modelling. <br />
<br />
But when I’m not at University... I’m a lover and addict of ''sports'', I like to listen music, to play ''djembes'', to spend time in front my laptop, and to lie in the sun. <br />
Can I recomend you a film?? -> [[Image:Pi1.jpg]]</div>Freestymhttp://2007.igem.org/wiki/index.php/User:FreestymUser:Freestym2007-07-20T01:22:28Z<p>Freestym: </p>
<hr />
<div>[[Image:Pi1.jpg]]<br />
<br />
Hey!<br />
<br />
I’m a student of '''Statistics''' from Spain ('''''Barcelona''''', UAB). I have just finished my degree at University of Glasgow and next year I’m going to do a Master by Research in Bioinformatics. My topics of interest are Time Series and Stochastic Modelling. <br />
<br />
But when I’m not at University... I’m a lover and addict of ''sports'', I like to listen music, to play ''djembes'', to spend time in front my laptop, and to lie in the sun. <br />
Can I recomend you a film?? -> [[Image:Pi1.jpg]]</div>Freestymhttp://2007.igem.org/wiki/index.php/User:FreestymUser:Freestym2007-07-20T01:22:12Z<p>Freestym: </p>
<hr />
<div>[[Image:Pi1.jpg]]<br />
<br />
Hey!<br />
<br />
I’m a student of '''Statistics''' from Spain ('''''Barcelona''''', UAB). I have just finished my degree at University of Glasgow and next year I’m going to do a Master by Research in Bioinformatics. My topics of interest are Time Series and Stochastic Modelling. <br />
<br />
But when I’m not at University... I’m a lover and addict of ''sports'', I like to listen music, to play ''djembes'', to spend time in front my laptop, and to lie in the sun. <br />
Can I recomend you a film?? -> [[Image:Pi1.jpg]x400]</div>Freestymhttp://2007.igem.org/wiki/index.php/User:FreestymUser:Freestym2007-07-20T01:21:20Z<p>Freestym: </p>
<hr />
<div>[[Image:Pi1.jpg]]<br />
<br />
Hey!<br />
<br />
I’m a student of '''Statistics''' from Spain ('''''Barcelona''''', UAB). I have just finished my degree at University of Glasgow and next year I’m going to do a Master by Research in Bioinformatics. My topics of interest are Time Series and Stochastic Modelling. <br />
<br />
But when I’m not at University... I’m a lover and addict of ''sports'', I like to listen music, to play ''djembes'', to spend time in front my laptop, and to lie in the sun. <br />
Can I recomend you a film?? -> Pi. [[Image:Pi1.jpg]]</div>Freestymhttp://2007.igem.org/wiki/index.php/File:Pi1.jpgFile:Pi1.jpg2007-07-20T01:19:24Z<p>Freestym: </p>
<hr />
<div></div>Freestymhttp://2007.igem.org/wiki/index.php/User:FreestymUser:Freestym2007-07-20T01:17:34Z<p>Freestym: </p>
<hr />
<div>[[Image:Example.jpg]]<br />
<br />
Hey!<br />
<br />
I’m a student of '''Statistics''' from Spain ('''''Barcelona''''', UAB). I have just finished my degree at University of Glasgow and next year I’m going to do a Master by Research in Bioinformatics. My topics of interest are Time Series and Stochastic Modelling. <br />
<br />
But when I’m not at University... I’m a lover and addict of ''sports'', I like to listen music, to play ''djembes'', to spend time in front my laptop, and to lie in the sun. <br />
Can I recomend you a film?? -> Pi. [[Image:Example.jpg]]</div>Freestymhttp://2007.igem.org/wiki/index.php/User:FreestymUser:Freestym2007-07-20T01:09:02Z<p>Freestym: </p>
<hr />
<div>Hey!<br />
<br />
I’m a student of '''Statistics''' from Spain ('''''Barcelona''''', UAB). I have just finished my degree at University of Glasgow and next year I’m going to do a Master by Research in Bioinformatics. My topics of interest are Time Series and Stochastic Modelling. <br />
<br />
But when I’m not at University... I’m a lover and addict of ''sports'', I like to listen music, to play ''djembes'', to spend time in front my laptop, and to lie in the sun. <br />
Can I recomend you a film?? -> Phi.</div>Freestymhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-12T09:23:04Z<p>Freestym: /* <u> Multiple Transcription Factors </u> */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
[[Image:simpledecay.jpg|400px]]<br />
<br />
[[Image:reversible.jpg|400px]]<br />
<br />
[[Image:addition.jpg|400px]]<br />
<br />
[[Image:enzyme.jpg|400px]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG | 700px]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in [[Mass-Action Reaction Modelling]] and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
=== Michaelis-Menten ===<br />
''This was taken from 'Biochemistry' by 'Stryer'''<br><br />
Anybody who has done any sort of biological study will know Michaelis-Menten what i am trying to acheive here is to take it from the basics so as to equate it to the equations we will be using to model the system and to give the biologists an idea of what values and models we need. In this case all k values are rate constants and [] means concentration and E is enzyme, S is substrate and [E]t is total enzyme concentration. <br><br />
The Michaelis-Menten equation describes the kinetic properties of many enzymes. Consider the simple system A -> P<br />
The rate of V is the quantity of A that disappears over a specified unit of time which is equal to the rate of appearance of P. For this system V=k[A] where k is the rate constant. <br />
The simplest model that accounts for the kinetic properties of many enzymes is (i will add it in when i have figured out how to)<br><br />
what we want is an expression that relates the rate of catalysis to the concentrations of substrate and enzyme and the rates of the individual steps.<br><br />
Our starting point is that the catalytic rate is equal to the product of the ES complex and k3.<br />
'''Vo=K2[ES]''' ''call this '''eqn(1)''' as i will be referring to it again''<br />
Now expressing [ES]in terms of known quantities the rates of '''formation''' and '''breakdown''' of [ES] are given by:<br />
'''formation [ES] = k1*[E]*[S]'''<br />
'''breakdown [ES] = (k2+k3)*[ES]'''<br />
A steady state occurs when the rates of formation and breakdown of the ES complex are equal, this gives the formula<br />
'''k1*[E]*[S]=(k2+k3)*[ES]'''<br />
which then gives <br />
'''[E][S] / [ES]=(k2+k3) / k1''' <br> <br />
This can be simplified by defining '''Km''' called the Michaelis constant<br><br />
'''Km = (k2+k3) / k1'''<br />
from this we get<br />
'''[ES] = [E][S] / Km''' ''call this '''eqn(2)''' as i will be referring to it again'' <br><br />
Now examining the numerator of this equation: because substrate is usually present at much higher concentrations than the enzyme, the concentration of uncombined substrate [S]is very nearly equal to the total substrate concentration. The concentration of enzyme [E] is equal to '''[E]t - [ES]''' now substituting this into ''eqn(2)'' and after some simplification we get<br />
'''[ES]=([E]t*[S]) / ([S]+Km)'''<br />
by substituting this expression into ''eqn(1)'' we get<br />
'''Vo = (k2[E]t*[S]) / ([s]+Km)'''<br />
The maximised rate Vmax is obtained when the catalytic sites on the enzyme are saturated with substrate i.e '''[ES] = [E]t''' thus<br />
'''Vmax = k2*[E]t<br />
this gives the Michaelis-Menten equation <br />
'''Vo = Vmax*([S] / ([S]+km)) ''' ''call this '''eqn(3)''' as i will refer to it again'' <br />
when '''[S]=Km''' then '''Vo = Vmax / 2'''. Thus Km is equal to the substrate concentration at which the reaction rate is half its maximal value.<br><br />
<br />
<br><br><br />
<br />
<br />
=== <u> Multiple Transcription Factors </u> ===<br />
<br />
There is an extension of the formulas from Michaelis-Menten, for '''multiple transcription factors'''. <br />
<br />
''Regulation of gene expression is controlled by the binding of transcription factors to specific DNA sequences in gene promoter regions. Multiple transcription factor binding events are involved in the regulation of cellular processes.'' <br />
<br />
<br />
When we have more than one '''transcription factor''' (TF) involved we can find two situations:<br><br />
(In this page we will study the scenario with only 2 transcription factors involved) <br />
<br />
- SUM Gate.<br><br />
- ADD Gate.<br />
<br />
<br />
<u>'''SUM Gate'''</u>: As the word refers in this situation the effect from multiple TFs is additive. That means that the transcription could be induced for one '''OR''' other factor (or both together). But we have to note in this point that it’s not necessary the presence of both of them.<br />
<br />
<u>'''ADD Gate'''</u>: Implies the situation where the effect from multiple TFs is multiplicative. That means that the transcription will be induced for one '''AND''' the other factor at the same time (both actuate together). Nottice that if one of them is not active the transcription will not be done.<br />
<br />
<center>[[Image:formulas.jpg|400px]]</center></div>Freestymhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-12T09:22:30Z<p>Freestym: /* Multiple Transcription Factors */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
[[Image:simpledecay.jpg|400px]]<br />
<br />
[[Image:reversible.jpg|400px]]<br />
<br />
[[Image:addition.jpg|400px]]<br />
<br />
[[Image:enzyme.jpg|400px]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG | 700px]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in [[Mass-Action Reaction Modelling]] and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
=== Michaelis-Menten ===<br />
''This was taken from 'Biochemistry' by 'Stryer'''<br><br />
Anybody who has done any sort of biological study will know Michaelis-Menten what i am trying to acheive here is to take it from the basics so as to equate it to the equations we will be using to model the system and to give the biologists an idea of what values and models we need. In this case all k values are rate constants and [] means concentration and E is enzyme, S is substrate and [E]t is total enzyme concentration. <br><br />
The Michaelis-Menten equation describes the kinetic properties of many enzymes. Consider the simple system A -> P<br />
The rate of V is the quantity of A that disappears over a specified unit of time which is equal to the rate of appearance of P. For this system V=k[A] where k is the rate constant. <br />
The simplest model that accounts for the kinetic properties of many enzymes is (i will add it in when i have figured out how to)<br><br />
what we want is an expression that relates the rate of catalysis to the concentrations of substrate and enzyme and the rates of the individual steps.<br><br />
Our starting point is that the catalytic rate is equal to the product of the ES complex and k3.<br />
'''Vo=K2[ES]''' ''call this '''eqn(1)''' as i will be referring to it again''<br />
Now expressing [ES]in terms of known quantities the rates of '''formation''' and '''breakdown''' of [ES] are given by:<br />
'''formation [ES] = k1*[E]*[S]'''<br />
'''breakdown [ES] = (k2+k3)*[ES]'''<br />
A steady state occurs when the rates of formation and breakdown of the ES complex are equal, this gives the formula<br />
'''k1*[E]*[S]=(k2+k3)*[ES]'''<br />
which then gives <br />
'''[E][S] / [ES]=(k2+k3) / k1''' <br> <br />
This can be simplified by defining '''Km''' called the Michaelis constant<br><br />
'''Km = (k2+k3) / k1'''<br />
from this we get<br />
'''[ES] = [E][S] / Km''' ''call this '''eqn(2)''' as i will be referring to it again'' <br><br />
Now examining the numerator of this equation: because substrate is usually present at much higher concentrations than the enzyme, the concentration of uncombined substrate [S]is very nearly equal to the total substrate concentration. The concentration of enzyme [E] is equal to '''[E]t - [ES]''' now substituting this into ''eqn(2)'' and after some simplification we get<br />
'''[ES]=([E]t*[S]) / ([S]+Km)'''<br />
by substituting this expression into ''eqn(1)'' we get<br />
'''Vo = (k2[E]t*[S]) / ([s]+Km)'''<br />
The maximised rate Vmax is obtained when the catalytic sites on the enzyme are saturated with substrate i.e '''[ES] = [E]t''' thus<br />
'''Vmax = k2*[E]t<br />
this gives the Michaelis-Menten equation <br />
'''Vo = Vmax*([S] / ([S]+km)) ''' ''call this '''eqn(3)''' as i will refer to it again'' <br />
when '''[S]=Km''' then '''Vo = Vmax / 2'''. Thus Km is equal to the substrate concentration at which the reaction rate is half its maximal value.<br><br />
<br />
=== <u> Multiple Transcription Factors </u> ===<br />
<br />
There is an extension of the formulas from Michaelis-Menten, for '''multiple transcription factors'''. <br />
<br />
''Regulation of gene expression is controlled by the binding of transcription factors to specific DNA sequences in gene promoter regions. Multiple transcription factor binding events are involved in the regulation of cellular processes.'' <br />
<br />
<br />
When we have more than one '''transcription factor''' (TF) involved we can find two situations:<br><br />
(In this page we will study the scenario with only 2 transcription factors involved) <br />
<br />
- SUM Gate.<br><br />
- ADD Gate.<br />
<br />
<br />
<u>'''SUM Gate'''</u>: As the word refers in this situation the effect from multiple TFs is additive. That means that the transcription could be induced for one '''OR''' other factor (or both together). But we have to note in this point that it’s not necessary the presence of both of them.<br />
<br />
<u>'''ADD Gate'''</u>: Implies the situation where the effect from multiple TFs is multiplicative. That means that the transcription will be induced for one '''AND''' the other factor at the same time (both actuate together). Nottice that if one of them is not active the transcription will not be done.<br />
<br />
<center>[[Image:formulas.jpg|400px]]</center></div>Freestymhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-12T09:16:54Z<p>Freestym: /* Multiple Transcription Factors */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
[[Image:simpledecay.jpg|400px]]<br />
<br />
[[Image:reversible.jpg|400px]]<br />
<br />
[[Image:addition.jpg|400px]]<br />
<br />
[[Image:enzyme.jpg|400px]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG | 700px]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in [[Mass-Action Reaction Modelling]] and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
=== Michaelis-Menten ===<br />
''This was taken from 'Biochemistry' by 'Stryer'''<br><br />
Anybody who has done any sort of biological study will know Michaelis-Menten what i am trying to acheive here is to take it from the basics so as to equate it to the equations we will be using to model the system and to give the biologists an idea of what values and models we need. In this case all k values are rate constants and [] means concentration and E is enzyme, S is substrate and [E]t is total enzyme concentration. <br><br />
The Michaelis-Menten equation describes the kinetic properties of many enzymes. Consider the simple system A -> P<br />
The rate of V is the quantity of A that disappears over a specified unit of time which is equal to the rate of appearance of P. For this system V=k[A] where k is the rate constant. <br />
The simplest model that accounts for the kinetic properties of many enzymes is (i will add it in when i have figured out how to)<br><br />
what we want is an expression that relates the rate of catalysis to the concentrations of substrate and enzyme and the rates of the individual steps.<br><br />
Our starting point is that the catalytic rate is equal to the product of the ES complex and k3.<br />
'''Vo=K2[ES]''' ''call this '''eqn(1)''' as i will be referring to it again''<br />
Now expressing [ES]in terms of known quantities the rates of '''formation''' and '''breakdown''' of [ES] are given by:<br />
'''formation [ES] = k1*[E]*[S]'''<br />
'''breakdown [ES] = (k2+k3)*[ES]'''<br />
A steady state occurs when the rates of formation and breakdown of the ES complex are equal, this gives the formula<br />
'''k1*[E]*[S]=(k2+k3)*[ES]'''<br />
which then gives <br />
'''[E][S] / [ES]=(k2+k3) / k1''' <br> <br />
This can be simplified by defining '''Km''' called the Michaelis constant<br><br />
'''Km = (k2+k3) / k1'''<br />
from this we get<br />
'''[ES] = [E][S] / Km''' ''call this '''eqn(2)''' as i will be referring to it again'' <br><br />
Now examining the numerator of this equation: because substrate is usually present at much higher concentrations than the enzyme, the concentration of uncombined substrate [S]is very nearly equal to the total substrate concentration. The concentration of enzyme [E] is equal to '''[E]t - [ES]''' now substituting this into ''eqn(2)'' and after some simplification we get<br />
'''[ES]=([E]t*[S]) / ([S]+Km)'''<br />
by substituting this expression into ''eqn(1)'' we get<br />
'''Vo = (k2[E]t*[S]) / ([s]+Km)'''<br />
The maximised rate Vmax is obtained when the catalytic sites on the enzyme are saturated with substrate i.e '''[ES] = [E]t''' thus<br />
'''Vmax = k2*[E]t<br />
this gives the Michaelis-Menten equation <br />
'''Vo = Vmax*([S] / ([S]+km)) ''' ''call this '''eqn(3)''' as i will refer to it again'' <br />
when '''[S]=Km''' then '''Vo = Vmax / 2'''. Thus Km is equal to the substrate concentration at which the reaction rate is half its maximal value.<br><br />
<br />
=== Multiple Transcription Factors ===<br />
<br />
There is an extension of the formulas from Michaelis-Menten, for '''multiple transcription factors'''. <br />
<br />
''Regulation of gene expression is controlled by the binding of transcription factors to specific DNA sequences in gene promoter regions. Multiple transcription factor binding events are involved in the regulation of cellular processes.'' <br />
<br />
<br />
When we have more than one '''transcription factor''' (TF) involved we can find two situations:<br><br />
(In this page we will study the scenario with only 2 transcription factors involved) <br />
<br />
- SUM Gate.<br><br />
- ADD Gate.<br />
<br />
<br />
'''SUM Gate''': As the word refers in this situation the effect from multiple TFs is additive. That means that the transcription could be induced for one '''OR''' other factor (or both together). But we have to note in this point that it’s not necessary the presence of both of them.<br />
<br />
'''ADD Gate''': Implies the situation where the effect from multiple TFs is multiplicative. That means that the transcription will be induced for one '''AND''' the other factor at the same time (both actuate together). Nottice that if one of them is not active the transcription will not be done.<br />
<br />
[[Image:formulas.jpg|400px]]</div>Freestymhttp://2007.igem.org/wiki/index.php/File:Formulas.jpgFile:Formulas.jpg2007-07-12T09:15:41Z<p>Freestym: </p>
<hr />
<div></div>Freestymhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-12T09:15:16Z<p>Freestym: /* Multiple Transcription Factors */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
[[Image:simpledecay.jpg|400px]]<br />
<br />
[[Image:reversible.jpg|400px]]<br />
<br />
[[Image:addition.jpg|400px]]<br />
<br />
[[Image:enzyme.jpg|400px]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG | 700px]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in [[Mass-Action Reaction Modelling]] and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
=== Michaelis-Menten ===<br />
''This was taken from 'Biochemistry' by 'Stryer'''<br><br />
Anybody who has done any sort of biological study will know Michaelis-Menten what i am trying to acheive here is to take it from the basics so as to equate it to the equations we will be using to model the system and to give the biologists an idea of what values and models we need. In this case all k values are rate constants and [] means concentration and E is enzyme, S is substrate and [E]t is total enzyme concentration. <br><br />
The Michaelis-Menten equation describes the kinetic properties of many enzymes. Consider the simple system A -> P<br />
The rate of V is the quantity of A that disappears over a specified unit of time which is equal to the rate of appearance of P. For this system V=k[A] where k is the rate constant. <br />
The simplest model that accounts for the kinetic properties of many enzymes is (i will add it in when i have figured out how to)<br><br />
what we want is an expression that relates the rate of catalysis to the concentrations of substrate and enzyme and the rates of the individual steps.<br><br />
Our starting point is that the catalytic rate is equal to the product of the ES complex and k3.<br />
'''Vo=K2[ES]''' ''call this '''eqn(1)''' as i will be referring to it again''<br />
Now expressing [ES]in terms of known quantities the rates of '''formation''' and '''breakdown''' of [ES] are given by:<br />
'''formation [ES] = k1*[E]*[S]'''<br />
'''breakdown [ES] = (k2+k3)*[ES]'''<br />
A steady state occurs when the rates of formation and breakdown of the ES complex are equal, this gives the formula<br />
'''k1*[E]*[S]=(k2+k3)*[ES]'''<br />
which then gives <br />
'''[E][S] / [ES]=(k2+k3) / k1''' <br> <br />
This can be simplified by defining '''Km''' called the Michaelis constant<br><br />
'''Km = (k2+k3) / k1'''<br />
from this we get<br />
'''[ES] = [E][S] / Km''' ''call this '''eqn(2)''' as i will be referring to it again'' <br><br />
Now examining the numerator of this equation: because substrate is usually present at much higher concentrations than the enzyme, the concentration of uncombined substrate [S]is very nearly equal to the total substrate concentration. The concentration of enzyme [E] is equal to '''[E]t - [ES]''' now substituting this into ''eqn(2)'' and after some simplification we get<br />
'''[ES]=([E]t*[S]) / ([S]+Km)'''<br />
by substituting this expression into ''eqn(1)'' we get<br />
'''Vo = (k2[E]t*[S]) / ([s]+Km)'''<br />
The maximised rate Vmax is obtained when the catalytic sites on the enzyme are saturated with substrate i.e '''[ES] = [E]t''' thus<br />
'''Vmax = k2*[E]t<br />
this gives the Michaelis-Menten equation <br />
'''Vo = Vmax*([S] / ([S]+km)) ''' ''call this '''eqn(3)''' as i will refer to it again'' <br />
when '''[S]=Km''' then '''Vo = Vmax / 2'''. Thus Km is equal to the substrate concentration at which the reaction rate is half its maximal value.<br><br />
<br />
=== Multiple Transcription Factors ===<br />
<br />
There is an extension of the formulas from Michaelis-Menten, for '''multiple transcription factors'''. <br />
<br />
''Regulation of gene expression is controlled by the binding of transcription factors to specific DNA sequences in gene promoter regions. Multiple transcription factor binding events are involved in the regulation of cellular processes.'' <br />
<br />
<br />
When we have more than one '''transcription factor''' (TF) involved we can find two situations:<br><br />
(In this page we will study the scenario with only 2 transcription factors involved) <br />
<br />
- SUM Gate.<br><br />
- ADD Gate.<br />
<br />
<br />
'''SUM Gate''': As the word refers in this situation the effect from multiple TFs is additive. That means that the transcription could be induced for one '''OR''' other factor (or both together). But we have to note in this point that it’s not necessary the presence of both of them.<br />
<br />
'''ADD Gate''': Implies the situation where the effect from multiple TFs is multiplicative. That means that the transcription will be induced for one '''AND''' the other factor at the same time (both actuate together). Nottice that if one of them is not active the transcription will not be done.<br />
<br />
[[Image:formulas.jpg]]</div>Freestymhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-12T09:08:07Z<p>Freestym: /* Multiple Transcription Factors */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
[[Image:simpledecay.jpg|400px]]<br />
<br />
[[Image:reversible.jpg|400px]]<br />
<br />
[[Image:addition.jpg|400px]]<br />
<br />
[[Image:enzyme.jpg|400px]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG | 700px]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in [[Mass-Action Reaction Modelling]] and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
=== Michaelis-Menten ===<br />
''This was taken from 'Biochemistry' by 'Stryer'''<br><br />
Anybody who has done any sort of biological study will know Michaelis-Menten what i am trying to acheive here is to take it from the basics so as to equate it to the equations we will be using to model the system and to give the biologists an idea of what values and models we need. In this case all k values are rate constants and [] means concentration and E is enzyme, S is substrate and [E]t is total enzyme concentration. <br><br />
The Michaelis-Menten equation describes the kinetic properties of many enzymes. Consider the simple system A -> P<br />
The rate of V is the quantity of A that disappears over a specified unit of time which is equal to the rate of appearance of P. For this system V=k[A] where k is the rate constant. <br />
The simplest model that accounts for the kinetic properties of many enzymes is (i will add it in when i have figured out how to)<br><br />
what we want is an expression that relates the rate of catalysis to the concentrations of substrate and enzyme and the rates of the individual steps.<br><br />
Our starting point is that the catalytic rate is equal to the product of the ES complex and k3.<br />
'''Vo=K2[ES]''' ''call this '''eqn(1)''' as i will be referring to it again''<br />
Now expressing [ES]in terms of known quantities the rates of '''formation''' and '''breakdown''' of [ES] are given by:<br />
'''formation [ES] = k1*[E]*[S]'''<br />
'''breakdown [ES] = (k2+k3)*[ES]'''<br />
A steady state occurs when the rates of formation and breakdown of the ES complex are equal, this gives the formula<br />
'''k1*[E]*[S]=(k2+k3)*[ES]'''<br />
which then gives <br />
'''[E][S] / [ES]=(k2+k3) / k1''' <br> <br />
This can be simplified by defining '''Km''' called the Michaelis constant<br><br />
'''Km = (k2+k3) / k1'''<br />
from this we get<br />
'''[ES] = [E][S] / Km''' ''call this '''eqn(2)''' as i will be referring to it again'' <br><br />
Now examining the numerator of this equation: because substrate is usually present at much higher concentrations than the enzyme, the concentration of uncombined substrate [S]is very nearly equal to the total substrate concentration. The concentration of enzyme [E] is equal to '''[E]t - [ES]''' now substituting this into ''eqn(2)'' and after some simplification we get<br />
'''[ES]=([E]t*[S]) / ([S]+Km)'''<br />
by substituting this expression into ''eqn(1)'' we get<br />
'''Vo = (k2[E]t*[S]) / ([s]+Km)'''<br />
The maximised rate Vmax is obtained when the catalytic sites on the enzyme are saturated with substrate i.e '''[ES] = [E]t''' thus<br />
'''Vmax = k2*[E]t<br />
this gives the Michaelis-Menten equation <br />
'''Vo = Vmax*([S] / ([S]+km)) ''' ''call this '''eqn(3)''' as i will refer to it again'' <br />
when '''[S]=Km''' then '''Vo = Vmax / 2'''. Thus Km is equal to the substrate concentration at which the reaction rate is half its maximal value.<br><br />
<br />
=== Multiple Transcription Factors ===<br />
<br />
There is an extension of the formulas from Michaelis-Menten, for '''multiple transcription factors'''. <br />
<br />
''Regulation of gene expression is controlled by the binding of transcription factors to specific DNA sequences in gene promoter regions. Multiple transcription factor binding events are involved in the regulation of cellular processes.'' <br />
<br />
<br />
When we have more than one '''transcription factor''' (TF) involved we can find two situations:<br><br />
(In this page we will study the scenario with only 2 transcription factors involved) <br />
<br />
- SUM Gate.<br><br />
- ADD Gate.<br />
<br />
<br />
'''SUM Gate''': As the word refers in this situation the effect from multiple TFs is additive. That means that the transcription could be induced for one '''OR''' other factor (or both together). But we have to note in this point that it’s not necessary the presence of both of them.<br />
<br />
'''ADD Gate''': Implies the situation where the effect from multiple TFs is multiplicative. That means that the transcription will be induced for one '''AND''' the other factor at the same time (both actuate together). Nottice that if one of them is not active the transcription will not be done.</div>Freestymhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-12T09:07:29Z<p>Freestym: /* Multiple Transcription Factors */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
[[Image:simpledecay.jpg|400px]]<br />
<br />
[[Image:reversible.jpg|400px]]<br />
<br />
[[Image:addition.jpg|400px]]<br />
<br />
[[Image:enzyme.jpg|400px]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG | 700px]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in [[Mass-Action Reaction Modelling]] and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
=== Michaelis-Menten ===<br />
''This was taken from 'Biochemistry' by 'Stryer'''<br><br />
Anybody who has done any sort of biological study will know Michaelis-Menten what i am trying to acheive here is to take it from the basics so as to equate it to the equations we will be using to model the system and to give the biologists an idea of what values and models we need. In this case all k values are rate constants and [] means concentration and E is enzyme, S is substrate and [E]t is total enzyme concentration. <br><br />
The Michaelis-Menten equation describes the kinetic properties of many enzymes. Consider the simple system A -> P<br />
The rate of V is the quantity of A that disappears over a specified unit of time which is equal to the rate of appearance of P. For this system V=k[A] where k is the rate constant. <br />
The simplest model that accounts for the kinetic properties of many enzymes is (i will add it in when i have figured out how to)<br><br />
what we want is an expression that relates the rate of catalysis to the concentrations of substrate and enzyme and the rates of the individual steps.<br><br />
Our starting point is that the catalytic rate is equal to the product of the ES complex and k3.<br />
'''Vo=K2[ES]''' ''call this '''eqn(1)''' as i will be referring to it again''<br />
Now expressing [ES]in terms of known quantities the rates of '''formation''' and '''breakdown''' of [ES] are given by:<br />
'''formation [ES] = k1*[E]*[S]'''<br />
'''breakdown [ES] = (k2+k3)*[ES]'''<br />
A steady state occurs when the rates of formation and breakdown of the ES complex are equal, this gives the formula<br />
'''k1*[E]*[S]=(k2+k3)*[ES]'''<br />
which then gives <br />
'''[E][S] / [ES]=(k2+k3) / k1''' <br> <br />
This can be simplified by defining '''Km''' called the Michaelis constant<br><br />
'''Km = (k2+k3) / k1'''<br />
from this we get<br />
'''[ES] = [E][S] / Km''' ''call this '''eqn(2)''' as i will be referring to it again'' <br><br />
Now examining the numerator of this equation: because substrate is usually present at much higher concentrations than the enzyme, the concentration of uncombined substrate [S]is very nearly equal to the total substrate concentration. The concentration of enzyme [E] is equal to '''[E]t - [ES]''' now substituting this into ''eqn(2)'' and after some simplification we get<br />
'''[ES]=([E]t*[S]) / ([S]+Km)'''<br />
by substituting this expression into ''eqn(1)'' we get<br />
'''Vo = (k2[E]t*[S]) / ([s]+Km)'''<br />
The maximised rate Vmax is obtained when the catalytic sites on the enzyme are saturated with substrate i.e '''[ES] = [E]t''' thus<br />
'''Vmax = k2*[E]t<br />
this gives the Michaelis-Menten equation <br />
'''Vo = Vmax*([S] / ([S]+km)) ''' ''call this '''eqn(3)''' as i will refer to it again'' <br />
when '''[S]=Km''' then '''Vo = Vmax / 2'''. Thus Km is equal to the substrate concentration at which the reaction rate is half its maximal value.<br><br />
<br />
=== Multiple Transcription Factors ===<br />
<br />
There is an extension of the formulas from Michaelis-Menten, for '''multiple transcription factors'''. <br />
<br />
''Regulation of gene expression is controlled by the binding of transcription factors to specific DNA sequences in gene promoter regions. Multiple transcription factor binding events are involved in the regulation of cellular processes.'' <br />
<br />
<br />
When we have more than one '''transcription factor''' (TF) involved we can find two situations:<br><br />
(In this page we will study the scenario with only 2 transcription factors involved) <br />
<br />
- SUM Gate.<br><br />
- ADD Gate.<br />
<br />
<br />
'''SUM gate''': As the word refers in this situation the effect from multiple TFs is additive. That means that the transcription could be induced for one '''OR''' other factor (or both together). But we have to note in this point that it’s not necessary the presence of both of them.<br />
<br />
'''ADD gate''': Implies the situation where the effect from multiple TFs is multiplicative. That means that the transcription will be induced for one '''AND''' the other factor at the same time (both actuate together). Nottice that if one of them is not active the transcription will not be done.</div>Freestymhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-12T09:00:39Z<p>Freestym: /* Application */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
[[Image:simpledecay.jpg|400px]]<br />
<br />
[[Image:reversible.jpg|400px]]<br />
<br />
[[Image:addition.jpg|400px]]<br />
<br />
[[Image:enzyme.jpg|400px]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG | 700px]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in [[Mass-Action Reaction Modelling]] and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
=== Michaelis-Menten ===<br />
''This was taken from 'Biochemistry' by 'Stryer'''<br><br />
Anybody who has done any sort of biological study will know Michaelis-Menten what i am trying to acheive here is to take it from the basics so as to equate it to the equations we will be using to model the system and to give the biologists an idea of what values and models we need. In this case all k values are rate constants and [] means concentration and E is enzyme, S is substrate and [E]t is total enzyme concentration. <br><br />
The Michaelis-Menten equation describes the kinetic properties of many enzymes. Consider the simple system A -> P<br />
The rate of V is the quantity of A that disappears over a specified unit of time which is equal to the rate of appearance of P. For this system V=k[A] where k is the rate constant. <br />
The simplest model that accounts for the kinetic properties of many enzymes is (i will add it in when i have figured out how to)<br><br />
what we want is an expression that relates the rate of catalysis to the concentrations of substrate and enzyme and the rates of the individual steps.<br><br />
Our starting point is that the catalytic rate is equal to the product of the ES complex and k3.<br />
'''Vo=K2[ES]''' ''call this '''eqn(1)''' as i will be referring to it again''<br />
Now expressing [ES]in terms of known quantities the rates of '''formation''' and '''breakdown''' of [ES] are given by:<br />
'''formation [ES] = k1*[E]*[S]'''<br />
'''breakdown [ES] = (k2+k3)*[ES]'''<br />
A steady state occurs when the rates of formation and breakdown of the ES complex are equal, this gives the formula<br />
'''k1*[E]*[S]=(k2+k3)*[ES]'''<br />
which then gives <br />
'''[E][S] / [ES]=(k2+k3) / k1''' <br> <br />
This can be simplified by defining '''Km''' called the Michaelis constant<br><br />
'''Km = (k2+k3) / k1'''<br />
from this we get<br />
'''[ES] = [E][S] / Km''' ''call this '''eqn(2)''' as i will be referring to it again'' <br><br />
Now examining the numerator of this equation: because substrate is usually present at much higher concentrations than the enzyme, the concentration of uncombined substrate [S]is very nearly equal to the total substrate concentration. The concentration of enzyme [E] is equal to '''[E]t - [ES]''' now substituting this into ''eqn(2)'' and after some simplification we get<br />
'''[ES]=([E]t*[S]) / ([S]+Km)'''<br />
by substituting this expression into ''eqn(1)'' we get<br />
'''Vo = (k2[E]t*[S]) / ([s]+Km)'''<br />
The maximised rate Vmax is obtained when the catalytic sites on the enzyme are saturated with substrate i.e '''[ES] = [E]t''' thus<br />
'''Vmax = k2*[E]t<br />
this gives the Michaelis-Menten equation <br />
'''Vo = Vmax*([S] / ([S]+km)) ''' ''call this '''eqn(3)''' as i will refer to it again'' <br />
when '''[S]=Km''' then '''Vo = Vmax / 2'''. Thus Km is equal to the substrate concentration at which the reaction rate is half its maximal value.<br><br />
<br />
=== MULTIPLE TRANSCRIPTION FACTORS ===<br />
<br />
There is an extension of the formulas from Michaelis-Menten, for '''multiple transcription factors'''. <br />
<br />
''Regulation of gene expression is controlled by the binding of transcription factors to specific DNA sequences in gene promoter regions. Multiple transcription factor binding events are involved in the regulation of cellular processes.'' <br />
<br />
<br />
When we have more than one '''transcription factor''' (TF) involved we can find two situations:<br />
(In this page we will study the scenario with only 2 transcription factors involved) <br />
<br />
- SUM gate.<br />
- ADD gate.<br />
<br />
<br />
'''SUM gate''': As the word refers in this situation the effect from multiple TFs is additive. That means that the transcription could be induced for one '''OR''' other factor (or both together). But we have to note in this point that it’s not necessary the presence of both of them.<br />
<br />
'''ADD gate''': Implies the situation where the effect from multiple TFs is multiplicative. That means that the transcription will be induced for one '''AND''' the other factor at the same time (both actuate together). Nottice that if one of them is not active the transcription will not be done.</div>Freestym