http://2007.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=20&target=Freestym&year=&month=2007.igem.org - User contributions [en]2024-03-29T15:51:59ZFrom 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>
<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 />
===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 />
----<br />
{| valign=top cellpadding=3<br />
|-<br />
[[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>
<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 &.. 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 />
<div>{| valign=top cellpadding=3<br />
|-<br />
!align=center|[https://2007.igem.org/Glasgow https://static.igem.org/mediawiki/2007/thumb/c/cc/Uog.jpg/50px-Uog.jpg] || [[Glasgow|<font face=georgia color=#3366CC size=4>Back To <br> Glasgow's <br> Main Page</font>]]|| [[Glasgow/Wetlab|<font face=georgia color=#3366CC size=4>Go To <br> Glasgow's <br> Wetlab Log</font>]]<br />
|}<br />
----<br />
{|cellspacing="6px" cellpadding="16" border="0" width="100%"<br />
|- align=center<br />
|[https://2007.igem.org/Glasgow/Modeling <font face=georgia color=#3366CC size=5><b>Modelling</b></font>]<br />
|[https://2007.igem.org/Glasgow/DryLog <font face=georgia color=#3366CC size=5><b>Log</b></font>]<br />
|[https://2007.igem.org/Glasgow/DryTutorials <font face=georgia color=#3366CC size=5><b>Tutorials</b></font>]<br />
|[https://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 [[https://static.igem.org/mediawiki/2007/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 />
|[https://2007.igem.org/Glasgow/Modeling <font face=georgia color=#3366CC size=5><b>Modelling</b></font>]<br />
|[https://2007.igem.org/Glasgow/DryLog <font face=georgia color=#3366CC size=5><b>Log</b></font>]<br />
|[https://2007.igem.org/Glasgow/DryTutorials <font face=georgia color=#3366CC size=5><b>Tutorials</b></font>]<br />
|[https://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>Freestym