http://2007.igem.org/wiki/index.php?title=Special:Contributions/Toby&feed=atom&limit=50&target=Toby&year=&month=2007.igem.org - User contributions [en]2024-03-28T21:12:56ZFrom 2007.igem.orgMediaWiki 1.16.5http://2007.igem.org/wiki/index.php/Glasgow/InterviewsGlasgow/Interviews2007-09-20T15:36:23Z<p>Toby: /* Toby Friend */</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/Meet the team|<font face=georgia color=#99CCFF size=4>Back To <br> The Team <br> Page</font>]]<br />
|}<br />
----<br />
== 59 Second Interviews ==<br />
Coming very soon.<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><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 />
=== 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 />
#'''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></div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/InterviewsGlasgow/Interviews2007-09-20T15:35:48Z<p>Toby: /* Toby Friend */</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/Meet the team|<font face=georgia color=#99CCFF size=4>Back To <br> The Team <br> Page</font>]]<br />
|}<br />
----<br />
== 59 Second Interviews ==<br />
Coming very soon.<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><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 />
=== 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 />
#'''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></div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/InterviewsGlasgow/Interviews2007-09-20T15:35:07Z<p>Toby: /* Toby Friend */</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/Meet the team|<font face=georgia color=#99CCFF size=4>Back To <br> The Team <br> Page</font>]]<br />
|}<br />
----<br />
== 59 Second Interviews ==<br />
Coming very soon.<br />
<br />
=== Toby Friend ===<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 />
<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><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 />
=== 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 />
#'''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></div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/InterviewsGlasgow/Interviews2007-09-20T15:33:09Z<p>Toby: /* Toby Friend */</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/Meet the team|<font face=georgia color=#99CCFF size=4>Back To <br> The Team <br> Page</font>]]<br />
|}<br />
----<br />
== 59 Second Interviews ==<br />
Coming very soon.<br />
<br />
=== Toby Friend ===<br />
#'''How are you today?'''<br><br />
A but achey and sneezy, but I'll get over it.<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 />
#'''What do you feel you have gained from working in the Glasgow iGEM Team?'''<br><br />
see 'How and why...'<br />
#'''Where do you see yourself two years from now?'''<br><br />
Deleting Spam from my email account.<br />
#'''If you had £50,000 to invest in science, what would you do with it?'''<br><br />
AI baby!<br />
#'''What has been your favourite iGEM moment so far?'''<br><br />
hackey-sack in the sun!<br />
#'''If you could be the inventor of anything, what would it be?'''<br><br />
AI baby!<br />
#'''What are you doing this weekend?'''<br><br />
Reading some books and tidying my neglected London bedroom.<br />
#'''Tell us a secret.'''<br><br />
ok, but this is between everyone in the world with internet access and me!...<br />
#'''Describe yourself in five words.'''<br><br />
My name is Toby Friend<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 />
<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><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 />
=== 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 />
#'''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></div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/ModelingGlasgow/Modeling2007-09-07T15:32:32Z<p>Toby: </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>]]<br />
|}<br />
----<br />
<br />
= Trial model for the PDntR|S promoter =<br />
<br />
The current model that will be used for modeling purposes will use the three following equations to model the simple system as shown in Figure 1. The reasons for using these modified equations are discussed below. <br />
<br />
<center>[[Image:screenshot1.jpg]]</center><br />
<br />
''Discussion''<br />
<br />
The equation for the change of DntR|S within the system could be modelled by Equation 4<br />
<br />
<center>[[Image:screenshot2.jpg]]</center><br />
<br />
At the beginning of the reaction DntR will have an unknown constant value as it cannot be measured physically in the laboratory. As the DntR will have a constant value the DntR and kb can be replaced by another constant kb’ as shown <br />
<br />
<center>[[Image:screenshot3.jpg]]</center><br />
<br />
By substituting Equation 5 into Equation 4 gives<br />
<br />
<center>[[Image:screenshot4.jpg]]</center><br />
<br />
However it is clear from Equation 6 that as the signal increases the DntR|S will increase without ever reaching a saturation limit. It was decided that the equation should be changed to utilize Michaelis-Menten. This means that a saturation limit will now be possible as shown in Equation 1.<br />
<br />
<br />
Next it is important to note that the signal equation includes a term for the degradation of the signal as this is possible in the physical model. This equation also includes a term for the binding and a term for the unbinding as shown in Equation 2. <br />
<br />
<br />
Also it should be noted that in this model XGAL is ignored, this is because the level of blue that is measured is proportional to the LacZ produced. By ignoring XGAL it will simplify the system equations.<br />
<br />
<br />
Another point to note is that in this model of the system the transcription and the translation steps have been ‘lumped’ together by using Michaelis-Menten rather than modeling these biological steps separately.<br />
<br />
<br />
<center>[[Image:Simplemodel.jpg|500px]]</center><br />
<center>Figure 1</center><br />
<br />
<br />
'''Minicap Sensitivity Analysis Program Package Abstract'''<br><br />
The Multi-Parametric and Initial Concentration Sensitivity analysis (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 />
<br />
To see the full PDF report on Minicap [[https://static.igem.org/mediawiki/2007/f/fb/Minicap.pdf click here]].</div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/ModelingGlasgow/Modeling2007-09-07T10:44:28Z<p>Toby: </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>]]<br />
|}<br />
----<br />
<br />
= Trial model for the PDntR|S promoter =<br />
<br />
The current model that will be used for modeling purposes will use the three following equations to model the simple system as shown in Figure 1. The reasons for using these modified equations are discussed below. <br />
<br />
<center>[[Image:screenshot1.jpg]]</center><br />
<br />
''Discussion''<br />
<br />
The equation for the change of DntR|S within the system could be modelled by Equation 4<br />
<br />
<center>[[Image:screenshot2.jpg]]</center><br />
<br />
At the beginning of the reaction DntR will have an unknown constant value as it cannot be measured physically in the laboratory. As the DntR will have a constant value the DntR and kb can be replaced by another constant kb’ as shown <br />
<br />
<center>[[Image:screenshot3.jpg]]</center><br />
<br />
By substituting Equation 5 into Equation 4 gives<br />
<br />
<center>[[Image:screenshot4.jpg]]</center><br />
<br />
However it is clear from Equation 6 that as the signal increases the DntR|S will increase without ever reaching a saturation limit. It was decided that the equation should be changed to utilize Michaelis-Menten. This means that a saturation limit will now be possible as shown in Equation 1.<br />
<br />
<br />
Next it is important to note that the signal equation includes a term for the degradation of the signal as this is possible in the physical model. This equation also includes a term for the binding and a term for the unbinding as shown in Equation 2. <br />
<br />
<br />
Also it should be noted that in this model XGAL is ignored, this is because the level of blue that is measured is proportional to the LacZ produced. By ignoring XGAL it will simplify the system equations.<br />
<br />
<br />
Another point to note is that in this model of the system the transcription and the translation steps have been ‘lumped’ together by using Michaelis-Menten rather than modeling these biological steps separately.<br />
<br />
<br />
<center>[[Image:Simplemodel.jpg|500px]]</center><br />
<center>Figure 1</center><br />
<br />
<br />
'''Minicap Sensitivity Analysis Program Package'''<br><br />
The Multi-Parametric and Initial concentration analysis Sensitivity (Minicap) package is a Matlab function which executes a chosen Dynamic or Stochastic system 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) usually termed MPSA, or initial values of the variables in the user's system (eg. initial substrate concentrations) termed 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 />
To see the full PDF report on Minicap [[https://static.igem.org/mediawiki/2007/f/fb/Minicap.pdf click here]].</div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/ModelingGlasgow/Modeling2007-09-07T10:42:56Z<p>Toby: </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>]]<br />
|}<br />
----<br />
<br />
= Trial model for the PDntR|S promoter =<br />
<br />
The current model that will be used for modeling purposes will use the three following equations to model the simple system as shown in Figure 1. The reasons for using these modified equations are discussed below. <br />
<br />
<center>[[Image:screenshot1.jpg]]</center><br />
<br />
''Discussion''<br />
<br />
The equation for the change of DntR|S within the system could be modelled by Equation 4<br />
<br />
<center>[[Image:screenshot2.jpg]]</center><br />
<br />
At the beginning of the reaction DntR will have an unknown constant value as it cannot be measured physically in the laboratory. As the DntR will have a constant value the DntR and kb can be replaced by another constant kb’ as shown <br />
<br />
<center>[[Image:screenshot3.jpg]]</center><br />
<br />
By substituting Equation 5 into Equation 4 gives<br />
<br />
<center>[[Image:screenshot4.jpg]]</center><br />
<br />
However it is clear from Equation 6 that as the signal increases the DntR|S will increase without ever reaching a saturation limit. It was decided that the equation should be changed to utilize Michaelis-Menten. This means that a saturation limit will now be possible as shown in Equation 1.<br />
<br />
<br />
Next it is important to note that the signal equation includes a term for the degradation of the signal as this is possible in the physical model. This equation also includes a term for the binding and a term for the unbinding as shown in Equation 2. <br />
<br />
<br />
Also it should be noted that in this model XGAL is ignored, this is because the level of blue that is measured is proportional to the LacZ produced. By ignoring XGAL it will simplify the system equations.<br />
<br />
<br />
Another point to note is that in this model of the system the transcription and the translation steps have been ‘lumped’ together by using Michaelis-Menten rather than modeling these biological steps separately.<br />
<br />
<br />
<center>[[Image:Simplemodel.jpg|500px]]</center><br />
<center>Figure 1</center><br />
<br />
<br />
'''Minicap Sensitivity Analysis Program Package'''<br><br />
The Multi-Parametric and Initial concentration analysis Sensitivity (Minicap) package is a Matlab function which executes a chosen Dynamic or Stochastic system 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) usually termed MPSA, or initial values of the variables in the user's system (eg. initial substrate concentrations) termed 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 />
To see the full PDF report on Minicap [[https://static.igem.org/mediawiki/2007/f/fb/Minicap.pdf| click here]].</div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/ModelingGlasgow/Modeling2007-09-07T10:38:44Z<p>Toby: </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>]]<br />
|}<br />
----<br />
<br />
= Trial model for the PDntR|S promoter =<br />
<br />
The current model that will be used for modeling purposes will use the three following equations to model the simple system as shown in Figure 1. The reasons for using these modified equations are discussed below. <br />
<br />
<center>[[Image:screenshot1.jpg]]</center><br />
<br />
''Discussion''<br />
<br />
The equation for the change of DntR|S within the system could be modelled by Equation 4<br />
<br />
<center>[[Image:screenshot2.jpg]]</center><br />
<br />
At the beginning of the reaction DntR will have an unknown constant value as it cannot be measured physically in the laboratory. As the DntR will have a constant value the DntR and kb can be replaced by another constant kb’ as shown <br />
<br />
<center>[[Image:screenshot3.jpg]]</center><br />
<br />
By substituting Equation 5 into Equation 4 gives<br />
<br />
<center>[[Image:screenshot4.jpg]]</center><br />
<br />
However it is clear from Equation 6 that as the signal increases the DntR|S will increase without ever reaching a saturation limit. It was decided that the equation should be changed to utilize Michaelis-Menten. This means that a saturation limit will now be possible as shown in Equation 1.<br />
<br />
<br />
Next it is important to note that the signal equation includes a term for the degradation of the signal as this is possible in the physical model. This equation also includes a term for the binding and a term for the unbinding as shown in Equation 2. <br />
<br />
<br />
Also it should be noted that in this model XGAL is ignored, this is because the level of blue that is measured is proportional to the LacZ produced. By ignoring XGAL it will simplify the system equations.<br />
<br />
<br />
Another point to note is that in this model of the system the transcription and the translation steps have been ‘lumped’ together by using Michaelis-Menten rather than modeling these biological steps separately.<br />
<br />
<br />
<center>[[Image:Simplemodel.jpg|500px]]</center><br />
<center>Figure 1</center><br />
<br />
<br />
'''Minicap Sensitivity Analysis Program Package'''<br><br />
The Multi-Parametric and Initial concentration analysis Sensitivity (Minicap) package is a Matlab function which executes a chosen Dynamic or Stochastic system 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) usually termed MPSA, or initial values of the variables in the user's system (eg. initial substrate concentrations) termed 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 />
To see the full PDF report on Minicap click here [[Minicap.pdf| click here]].</div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/ModelingGlasgow/Modeling2007-09-07T10:34:56Z<p>Toby: </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>]]<br />
|}<br />
----<br />
<br />
= Trial model for the PDntR|S promoter =<br />
<br />
The current model that will be used for modeling purposes will use the three following equations to model the simple system as shown in Figure 1. The reasons for using these modified equations are discussed below. <br />
<br />
<center>[[Image:screenshot1.jpg]]</center><br />
<br />
''Discussion''<br />
<br />
The equation for the change of DntR|S within the system could be modelled by Equation 4<br />
<br />
<center>[[Image:screenshot2.jpg]]</center><br />
<br />
At the beginning of the reaction DntR will have an unknown constant value as it cannot be measured physically in the laboratory. As the DntR will have a constant value the DntR and kb can be replaced by another constant kb’ as shown <br />
<br />
<center>[[Image:screenshot3.jpg]]</center><br />
<br />
By substituting Equation 5 into Equation 4 gives<br />
<br />
<center>[[Image:screenshot4.jpg]]</center><br />
<br />
However it is clear from Equation 6 that as the signal increases the DntR|S will increase without ever reaching a saturation limit. It was decided that the equation should be changed to utilize Michaelis-Menten. This means that a saturation limit will now be possible as shown in Equation 1.<br />
<br />
<br />
Next it is important to note that the signal equation includes a term for the degradation of the signal as this is possible in the physical model. This equation also includes a term for the binding and a term for the unbinding as shown in Equation 2. <br />
<br />
<br />
Also it should be noted that in this model XGAL is ignored, this is because the level of blue that is measured is proportional to the LacZ produced. By ignoring XGAL it will simplify the system equations.<br />
<br />
<br />
Another point to note is that in this model of the system the transcription and the translation steps have been ‘lumped’ together by using Michaelis-Menten rather than modeling these biological steps separately.<br />
<br />
<br />
<center>[[Image:Simplemodel.jpg|500px]]</center><br />
<center>Figure 1</center><br />
<br />
<br />
'''Minicap Sensitivity Analysis Program Package'''<br><br />
The Multi-Parametric and Initial concentration analysis Sensitivity (Minicap) package is a Matlab function which executes a chosen Dynamic or Stochastic system 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) usually termed MPSA, or initial values of the variables in the user's system (eg. initial substrate concentrations) termed 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 />
To see the full PDF report on Minicap click here. [[Minicap.pdf| click here]]</div>Tobyhttp://2007.igem.org/wiki/index.php/File:Minicap.pdfFile:Minicap.pdf2007-09-07T10:33:31Z<p>Toby: </p>
<hr />
<div></div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/ModelingGlasgow/Modeling2007-09-07T10:32:31Z<p>Toby: </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>]]<br />
|}<br />
----<br />
<br />
= Trial model for the PDntR|S promoter =<br />
<br />
The current model that will be used for modeling purposes will use the three following equations to model the simple system as shown in Figure 1. The reasons for using these modified equations are discussed below. <br />
<br />
<center>[[Image:screenshot1.jpg]]</center><br />
<br />
''Discussion''<br />
<br />
The equation for the change of DntR|S within the system could be modelled by Equation 4<br />
<br />
<center>[[Image:screenshot2.jpg]]</center><br />
<br />
At the beginning of the reaction DntR will have an unknown constant value as it cannot be measured physically in the laboratory. As the DntR will have a constant value the DntR and kb can be replaced by another constant kb’ as shown <br />
<br />
<center>[[Image:screenshot3.jpg]]</center><br />
<br />
By substituting Equation 5 into Equation 4 gives<br />
<br />
<center>[[Image:screenshot4.jpg]]</center><br />
<br />
However it is clear from Equation 6 that as the signal increases the DntR|S will increase without ever reaching a saturation limit. It was decided that the equation should be changed to utilize Michaelis-Menten. This means that a saturation limit will now be possible as shown in Equation 1.<br />
<br />
<br />
Next it is important to note that the signal equation includes a term for the degradation of the signal as this is possible in the physical model. This equation also includes a term for the binding and a term for the unbinding as shown in Equation 2. <br />
<br />
<br />
Also it should be noted that in this model XGAL is ignored, this is because the level of blue that is measured is proportional to the LacZ produced. By ignoring XGAL it will simplify the system equations.<br />
<br />
<br />
Another point to note is that in this model of the system the transcription and the translation steps have been ‘lumped’ together by using Michaelis-Menten rather than modeling these biological steps separately.<br />
<br />
<br />
<center>[[Image:Simplemodel.jpg|500px]]</center><br />
<center>Figure 1</center><br />
<br />
<br />
'''Minicap Sensitivity Analysis Program Package'''<br><br />
The Multi-Parametric and Initial concentration analysis Sensitivity (Minicap) package is a Matlab function which executes a chosen Dynamic or Stochastic system 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) usually termed MPSA, or initial values of the variables in the user's system (eg. initial substrate concentrations) termed 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 />
To see the full PDF report on Minicap click here. [[Glasgow/|<font face=georgia color=#3366CC size=4> Read Toby's <br> 59 Second <br> Interview </font>]]</div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/ModelingGlasgow/Modeling2007-09-07T10:31:30Z<p>Toby: </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>]]<br />
|}<br />
----<br />
<br />
= Trial model for the PDntR|S promoter =<br />
<br />
The current model that will be used for modeling purposes will use the three following equations to model the simple system as shown in Figure 1. The reasons for using these modified equations are discussed below. <br />
<br />
<center>[[Image:screenshot1.jpg]]</center><br />
<br />
''Discussion''<br />
<br />
The equation for the change of DntR|S within the system could be modelled by Equation 4<br />
<br />
<center>[[Image:screenshot2.jpg]]</center><br />
<br />
At the beginning of the reaction DntR will have an unknown constant value as it cannot be measured physically in the laboratory. As the DntR will have a constant value the DntR and kb can be replaced by another constant kb’ as shown <br />
<br />
<center>[[Image:screenshot3.jpg]]</center><br />
<br />
By substituting Equation 5 into Equation 4 gives<br />
<br />
<center>[[Image:screenshot4.jpg]]</center><br />
<br />
However it is clear from Equation 6 that as the signal increases the DntR|S will increase without ever reaching a saturation limit. It was decided that the equation should be changed to utilize Michaelis-Menten. This means that a saturation limit will now be possible as shown in Equation 1.<br />
<br />
<br />
Next it is important to note that the signal equation includes a term for the degradation of the signal as this is possible in the physical model. This equation also includes a term for the binding and a term for the unbinding as shown in Equation 2. <br />
<br />
<br />
Also it should be noted that in this model XGAL is ignored, this is because the level of blue that is measured is proportional to the LacZ produced. By ignoring XGAL it will simplify the system equations.<br />
<br />
<br />
Another point to note is that in this model of the system the transcription and the translation steps have been ‘lumped’ together by using Michaelis-Menten rather than modeling these biological steps separately.<br />
<br />
<br />
<center>[[Image:Simplemodel.jpg|500px]]</center><br />
<center>Figure 1</center><br />
<br />
<br />
'''Minicap Sensitivity Analysis Program Package'''<br><br />
The Multi-Parametric and Initial concentration analysis Sensitivity (Minicap) package is a Matlab function which executes a chosen Dynamic or Stochastic system 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) usually termed MPSA, or initial values of the variables in the user's system (eg. initial substrate concentrations) termed 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 />
To see the full PDF report on Minicap click here. [[Glasgow/|<font face=georgia color=#3366CC size=4> Read Toby's <br> 59 Second <br> Interview </font>]]</div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-17T09:34:48Z<p>Toby: /* 16/08 */</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 />
=== 08/08 ===<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 />
Here I come to enlighten the oblivious. ''lhsdesign()'' in MATLAB is very slow for some reason. Moreover it seems to have polynomial complexity in number of samples while having linear complexity in number of dimensions. [[Image:Glasgow_lhs_execution.png|frame|right|Execution times for MATLAB's lhsdesign(). Slopes along x axis are straight (linear complexity), slopes along y axis are curved indicating polynomial complexity. The value for (20,6000) is unknown due to memory paging - indicated by a thunder.]] At some point (e.g. 6000 samples in 20 dimensions) it also uses so much memory that a 1GB RAM Windows machine starts to page and effectively brings the computation to a halt. In the multi-parametrix analysis creating a hypercube has become a limiting factor for the size of our computations. This is unacceptable!<br />
<br />
Why do we need so many samples anyway? Well, if you take 3 dimensional space and you take 1000 samples it will be only 10 samples along each axis! What if we want to have ONLY 10 samples along each axis in 21 dimensions? Well, we'll need 1e21 samples, oh! <br />
<br />
A quick Google search led us to a mathematical library webpage at [http://www.scs.fsu.edu/ Florida State University] where a [http://people.scs.fsu.edu/~burkardt/cpp_src/latin_random/latin_random.html C++ code for generating samples from latin hypercube] is available. A big hand for them. We have tortured the latin_random_prb.C example file to create an interface and finally call it lhsdesign.c. It takes the number of samples and number of dimensions as command line arguments and writes the samples to standard output in a format that ''csvread'' likes. Inside MATLAB the file supadupalhsdesign.m provides the same interface as ''lhsdesign()'':<br />
<br> <br> <br><br />
<br> <br> <br> <br><br />
<code><br />
function samples = supadupalhsdesign(numsamples, numdimentions)<br />
system(['lhsdesign.exe ', num2str(numsamples),' ', num2str(numdimentions), ' > lhsout.csv']);<br />
samples = csvread('lhsout.csv');<br />
end<br />
</code><br />
[[Image:Glasgow_slhs_execution.png|frame|right|Execution times of the supadupalhsdesign.m averaged over 10 runs (it was a little bit shaky due to disk I/O effects). We can see that it is much faster.]]<br />
What happens is the lhsdesign.exe is called using the ''system'' command and its output is directed to a temporary .csv file. Then the file is read into a matrix by ''csvread''. Unfortunately we were not able to find a way to take the standard output of a command into a matrix directly, but it's not a major problem.<br />
<br />
It's no rocket science, although [[User:0602359k|Karolis]] says that rocket science is actually not so hard ;)<br />
[[User:Mcek|Mcek]]<br />
<br />
'''UPDATE 14/08:''' The C++ code for latin hypercube sampling wouldn't generate 200000 samples for 21 dimensions excusing itself with stack overflow. A look inside revealed that the array that stores the samples was static. A very quick <br />
<code> <br />
double* x = NULL;<br />
x = new double[DIM_NUM*POINT_NUM];<br />
...<br />
delete[] x;<br />
x = NULL;<br />
</code><br />
fix was needed to allocate the array dynamically and our program is happy to give us 1 million samples in 23 dimensions and surely more!<br />
[[User:Mcek|Mcek]]<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 />
All tests we were running today points that, we need to adjust our model ‘One Big F’, because model ‘F3 feedback; shows no influence for the final output. Wet lab said that they expect that ‘F3 feedback’ would change the repose in general. We have few, that still believe in parameter search, but their numbers are dwindling….<br />
<br />
=== 15/08 ===<br />
With the help of David we managed to find few more constants for our models, he also noted that some minor changes to model will have to be made because last mass action is believed to be unstable and could not be modeled separately.<br />
<br />
=== 16/08 ===<br />
The Multi-Parametric Sensitivity Analysis program is now (basically) complete. It is a marvel of computing beauty and shows how adaptable and smart graduates of Product Design Engineering are. A separate link for the program is being generated...!<br />
<br />
=== 17/08 ===<br />
?</div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-08-17T09:34:37Z<p>Toby: /* 16/08 */</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 />
=== 08/08 ===<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 />
Here I come to enlighten the oblivious. ''lhsdesign()'' in MATLAB is very slow for some reason. Moreover it seems to have polynomial complexity in number of samples while having linear complexity in number of dimensions. [[Image:Glasgow_lhs_execution.png|frame|right|Execution times for MATLAB's lhsdesign(). Slopes along x axis are straight (linear complexity), slopes along y axis are curved indicating polynomial complexity. The value for (20,6000) is unknown due to memory paging - indicated by a thunder.]] At some point (e.g. 6000 samples in 20 dimensions) it also uses so much memory that a 1GB RAM Windows machine starts to page and effectively brings the computation to a halt. In the multi-parametrix analysis creating a hypercube has become a limiting factor for the size of our computations. This is unacceptable!<br />
<br />
Why do we need so many samples anyway? Well, if you take 3 dimensional space and you take 1000 samples it will be only 10 samples along each axis! What if we want to have ONLY 10 samples along each axis in 21 dimensions? Well, we'll need 1e21 samples, oh! <br />
<br />
A quick Google search led us to a mathematical library webpage at [http://www.scs.fsu.edu/ Florida State University] where a [http://people.scs.fsu.edu/~burkardt/cpp_src/latin_random/latin_random.html C++ code for generating samples from latin hypercube] is available. A big hand for them. We have tortured the latin_random_prb.C example file to create an interface and finally call it lhsdesign.c. It takes the number of samples and number of dimensions as command line arguments and writes the samples to standard output in a format that ''csvread'' likes. Inside MATLAB the file supadupalhsdesign.m provides the same interface as ''lhsdesign()'':<br />
<br> <br> <br><br />
<br> <br> <br> <br><br />
<code><br />
function samples = supadupalhsdesign(numsamples, numdimentions)<br />
system(['lhsdesign.exe ', num2str(numsamples),' ', num2str(numdimentions), ' > lhsout.csv']);<br />
samples = csvread('lhsout.csv');<br />
end<br />
</code><br />
[[Image:Glasgow_slhs_execution.png|frame|right|Execution times of the supadupalhsdesign.m averaged over 10 runs (it was a little bit shaky due to disk I/O effects). We can see that it is much faster.]]<br />
What happens is the lhsdesign.exe is called using the ''system'' command and its output is directed to a temporary .csv file. Then the file is read into a matrix by ''csvread''. Unfortunately we were not able to find a way to take the standard output of a command into a matrix directly, but it's not a major problem.<br />
<br />
It's no rocket science, although [[User:0602359k|Karolis]] says that rocket science is actually not so hard ;)<br />
[[User:Mcek|Mcek]]<br />
<br />
'''UPDATE 14/08:''' The C++ code for latin hypercube sampling wouldn't generate 200000 samples for 21 dimensions excusing itself with stack overflow. A look inside revealed that the array that stores the samples was static. A very quick <br />
<code> <br />
double* x = NULL;<br />
x = new double[DIM_NUM*POINT_NUM];<br />
...<br />
delete[] x;<br />
x = NULL;<br />
</code><br />
fix was needed to allocate the array dynamically and our program is happy to give us 1 million samples in 23 dimensions and surely more!<br />
[[User:Mcek|Mcek]]<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 />
All tests we were running today points that, we need to adjust our model ‘One Big F’, because model ‘F3 feedback; shows no influence for the final output. Wet lab said that they expect that ‘F3 feedback’ would change the repose in general. We have few, that still believe in parameter search, but their numbers are dwindling….<br />
<br />
=== 15/08 ===<br />
With the help of David we managed to find few more constants for our models, he also noted that some minor changes to model will have to be made because last mass action is believed to be unstable and could not be modeled separately.<br />
<br />
=== 16/08 ===<br />
The Multi-Parametric Sensetivity Analysis program is now (basically) complete. It is a marvel of computing beauty and shows how adaptable and smart graduates of Product Design Engineering are. A separate link for the program is being generated...!<br />
<br />
=== 17/08 ===<br />
?</div>Tobyhttp://2007.igem.org/wiki/index.php/GlasgowGlasgow2007-07-26T14:13:04Z<p>Toby: </p>
<hr />
<div>[[Image:Glasgow header.png]]<br />
<center>[[Image:Logo_d.png|650px]]</center><br />
{| cellspacing="6px" cellpadding="16" border="0" width="100%"<br />
|-<br />
|[[Glasgow/Background|BACKGROUND]]<br />
|[[Glasgow/Plan|PHASES]]<br />
|[[Glasgow/Meet_the_team|MEET THE TEAM]]<br />
|<center>[[Glasgow/Drylab|DRYLAB LOG]]<br> [[Glasgow/Modeling|MODELLING]]</center><br />
|[[Glasgow/Wetlab|WETLAB]]<br />
|[[Glasgow/Lectures|TUTORIALS]]<br />
|}<br />
<br />
== Links to our Sponsors ==<br />
[http://www.gla.ac.uk http://ultragrid.east.isi.edu/images/glasgow-logo.png]<br />
[http://www.scottish-enterprise.com/ http://www.conscia.co.uk/images/logo/se.gif]<br />
[http://www.anachem.co.uk http://www.pro-4-pro.com/media/company/anachem_logo.jpg] <br><br />
[http://www.merck.com/ http://www.v2020.org/library-media/images/Merck.jpg]<br />
[http://www.ethz.ch/index_EN http://www.photogrammetry.ethz.ch/logos/eth-logo-140.gif]</div>Tobyhttp://2007.igem.org/wiki/index.php/File:Logo_d.pngFile:Logo d.png2007-07-26T14:09:58Z<p>Toby: </p>
<hr />
<div></div>Tobyhttp://2007.igem.org/wiki/index.php/File:Logo_d.pdfFile:Logo d.pdf2007-07-26T10:06:58Z<p>Toby: </p>
<hr />
<div></div>Tobyhttp://2007.igem.org/wiki/index.php/GlasgowGlasgow2007-07-25T15:43:51Z<p>Toby: </p>
<hr />
<div>[[Image:Glasgow header.png]]<br />
<center>[[Image:Logo_glasgow.jpg|650px]]</center><br />
{| cellspacing="6px" cellpadding="16" border="0" width="100%"<br />
|-<br />
|[[Glasgow/Background|BACKGROUND]]<br />
|[[Glasgow/Plan|PHASES]]<br />
|[[Glasgow/Meet_the_team|MEET THE TEAM]]<br />
|<center>[[Glasgow/Drylab|DRYLAB LOG]]<br> [[Glasgow/Modeling|MODELLING]]</center><br />
|[[Glasgow/Wetlab|WETLAB]]<br />
|[[Glasgow/Lectures|TUTORIALS]]<br />
|}<br />
<br />
== Links to our Sponsors ==<br />
[http://www.gla.ac.uk http://ultragrid.east.isi.edu/images/glasgow-logo.png]<br />
[http://www.scottish-enterprise.com/ http://www.conscia.co.uk/images/logo/se.gif]<br />
[http://www.anachem.co.uk http://www.pro-4-pro.com/media/company/anachem_logo.jpg] <br><br />
[http://www.merck.com/ http://www.v2020.org/library-media/images/Merck.jpg]<br />
[http://www.ethz.ch/index_EN http://www.photogrammetry.ethz.ch/logos/eth-logo-140.gif]</div>Tobyhttp://2007.igem.org/wiki/index.php/GlasgowGlasgow2007-07-20T09:00:02Z<p>Toby: /* Links to our Sponsers */</p>
<hr />
<div>[[Image:Glasgow header.png]]<br />
<center>[[Image:Logo_glasgow.jpg|650px]]<br />
{| cellspacing="6px" cellpadding="16" border="0" width="100%"<br />
|-<br />
|[[Glasgow/Background|BACKGROUND]]<br />
|[[Glasgow/Plan|PHASES]]<br />
|[[Glasgow/Meet_the_team|MEET THE TEAM]]<br />
|[[Glasgow/Drylab|DRYLAB]]<br />
|[[Glasgow/Wetlab|WETLAB]]<br />
|[[Glasgow/Lectures|TUTORIALS]]<br />
|}<br />
<br />
== Links to our Sponsors ==<br />
[http://www.gla.ac.uk http://ultragrid.east.isi.edu/images/glasgow-logo.png]<br />
[http://www.scottish-enterprise.com/ http://www.conscia.co.uk/images/logo/se.gif]<br />
[http://www.anachem.co.uk http://www.pro-4-pro.com/media/company/anachem_logo.jpg]<br />
[http://www.merck.com/ http://www.v2020.org/library-media/images/Merck.jpg]<br />
[http://www.ethz.ch/index_EN http://www.photogrammetry.ethz.ch/logos/eth-logo-140.gif]</div>Tobyhttp://2007.igem.org/wiki/index.php/GlasgowGlasgow2007-07-20T08:56:49Z<p>Toby: </p>
<hr />
<div>[[Image:Glasgow header.png]]<br />
<center>[[Image:Logo_glasgow.jpg|650px]]<br />
{| cellspacing="6px" cellpadding="16" border="0" width="100%"<br />
|-<br />
|[[Glasgow/Background|BACKGROUND]]<br />
|[[Glasgow/Plan|PHASES]]<br />
|[[Glasgow/Meet_the_team|MEET THE TEAM]]<br />
|[[Glasgow/Drylab|DRYLAB]]<br />
|[[Glasgow/Wetlab|WETLAB]]<br />
|[[Glasgow/Lectures|TUTORIALS]]<br />
|}<br />
<br />
== Links to our Sponsers ==<br />
[http://www.gla.ac.uk http://ultragrid.east.isi.edu/images/glasgow-logo.png]<br />
[http://www.scottish-enterprise.com/ http://www.conscia.co.uk/images/logo/se.gif]<br />
[http://www.anachem.co.uk http://www.pro-4-pro.com/media/company/anachem_logo.jpg]<br />
[http://www.merck.com/ http://www.v2020.org/library-media/images/Merck.jpg]<br />
[http://www.ethz.ch/index_EN http://www.photogrammetry.ethz.ch/logos/eth-logo-140.gif]</div>Tobyhttp://2007.igem.org/wiki/index.php/File:Logo_glasgow.jpgFile:Logo glasgow.jpg2007-07-20T08:54:09Z<p>Toby: </p>
<hr />
<div></div>Tobyhttp://2007.igem.org/wiki/index.php/GlasgowGlasgow2007-07-20T08:53:56Z<p>Toby: </p>
<hr />
<div>[[Image:Glasgow header.png]]<br />
[[Image:Logo_glasgow.jpg]]<br />
{| cellspacing="6px" cellpadding="16" border="0" width="100%"<br />
|-<br />
|[[Glasgow/Background|BACKGROUND]]<br />
|[[Glasgow/Plan|PHASES]]<br />
|[[Glasgow/Meet_the_team|MEET THE TEAM]]<br />
|[[Glasgow/Drylab|DRYLAB]]<br />
|[[Glasgow/Wetlab|WETLAB]]<br />
|[[Glasgow/Lectures|TUTORIALS]]<br />
|}<br />
<br />
== Links to our Sponsers ==<br />
[http://www.gla.ac.uk http://ultragrid.east.isi.edu/images/glasgow-logo.png]<br />
[http://www.scottish-enterprise.com/ http://www.conscia.co.uk/images/logo/se.gif]<br />
[http://www.anachem.co.uk http://www.pro-4-pro.com/media/company/anachem_logo.jpg]<br />
[http://www.merck.com/ http://www.v2020.org/library-media/images/Merck.jpg]<br />
[http://www.ethz.ch/index_EN http://www.photogrammetry.ethz.ch/logos/eth-logo-140.gif]</div>Tobyhttp://2007.igem.org/wiki/index.php/File:Logo.pdfFile:Logo.pdf2007-07-20T08:44:01Z<p>Toby: </p>
<hr />
<div></div>Tobyhttp://2007.igem.org/wiki/index.php/GlasgowGlasgow2007-07-20T08:27:46Z<p>Toby: /* Links */</p>
<hr />
<div>[[Image:Glasgow header.png]]<br />
{| cellspacing="6px" cellpadding="16" border="0" width="100%"<br />
|-<br />
|[[Glasgow/Background|BACKGROUND]]<br />
|[[Glasgow/Plan|PHASES]]<br />
|[[Glasgow/Meet_the_team|MEET THE TEAM]]<br />
|[[Glasgow/Drylab|DRYLAB]]<br />
|[[Glasgow/Wetlab|WETLAB]]<br />
|[[Glasgow/Lectures|TUTORIALS]]<br />
|}<br />
<br />
== Links to our Sponsers ==<br />
[http://www.gla.ac.uk http://ultragrid.east.isi.edu/images/glasgow-logo.png]<br />
[http://www.scottish-enterprise.com/ http://www.conscia.co.uk/images/logo/se.gif]<br />
[http://www.anachem.co.uk http://www.pro-4-pro.com/media/company/anachem_logo.jpg]<br />
[http://www.merck.com/ http://www.v2020.org/library-media/images/Merck.jpg]<br />
[http://www.ethz.ch/index_EN http://www.photogrammetry.ethz.ch/logos/eth-logo-140.gif]</div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/DrylabGlasgow/Drylab2007-07-20T08:22:38Z<p>Toby: </p>
<hr />
<div>== Week 1 ==<br />
=== 02/07 ===<br />
After a brief re-introduction to the Laboratory and our project proposal, we outlined a 6-PHASE approach to guide our practice over the summer.<br />
<br />
From here the Modellers began working on basic Matlab modelling tutorials, designed by Xu Gu, to allow all modellers to reach a satisfactory ability. By the end of the day we had completed a number of Mass-action programs using the ode45 funtion and grasped the translation from basic notaion into Substrate, Enzyme and S/E-complex notation.<br />
<br />
=== 03/07 ===<br />
We developed our modelling techniques by programming responses to basic metabolic and signalling pathways. We then learnt more precise techniques of modelling, e.g. accuracy and tolerace variance and noting parameters. We then covered Loop and Switch functions.<br />
<br />
=== 04/07 ===<br />
We are were introduced to the Nested function to allow for simpler programming, and the basic ideas behind Sensitivity of output due to a range of possible values of varying constants.<br />
<br />
In the afternoon, all modellers were shown some Wetlab techniques for the sake of a more thorough understanding of the processes involved.<br />
<br />
Our experiment was to extract plasmids from a number of different bacterial cultures.<br />
<br />
=== 05/07 ===<br />
blank<br />
<br />
=== 06/07 ===<br />
Raya Khanin introduced us to the Michaelis-Menton equation and its use in biochemical process modelling. We then discussed the methods of modelling different promoters's 'Acceptablility', i.e. 'And', 'Or' and 'Sum'.<br />
<br />
== Week 2 ==<br />
=== 09/07 ===<br />
Our first step towards modelling a possible method for PHASE 1.<br />
<br />
=== 10/07 ===<br />
We planned and gave a lecture to those in Wetlab explaining the methods we employ as modellers to represent various biochemical reactions. We also received a complementary lecture from those in Wetlab explaining the processes they employ to carry out and observe experimentation.<br />
[[User:Toby|Toby]] 11:27, 11 July 2007 (EDT)<br />
<br />
=== 11/07 ===<br />
We have finally agreed on model we are going to simulate, but wet lab updated us, that first experiment went wrong and we have to remodel. First few minutes after such news were shocking. It took me an hour to finalize all the details. And now I have to go again.<br><br />
Lucky for us modelers, computers dot care much about bacteria used in experiment so as long as we follow the same path we only need to rename variables. Bless! <br />
<br />
=== 12/07 ===<br />
A day dedicated to manual math as Rachel and Kristin does some analytical derivations for our models optimization. To be honest, we were very optimistic about the outcome, and though the formula derived were fine, and simulations went on as smoothly as ever, the optimization part shoved that 9 dimensional space is though nut to crack even for MatLAB. <br><br />
<br />
--[[User:0602359k|Karolis]] 04:53, 13 July 2007 (EDT)</div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/Meet_the_teamGlasgow/Meet the team2007-07-13T16:14:00Z<p>Toby: </p>
<hr />
<div><center>[[Image:Glasgow team photo.jpg|600px]]<br><br />
<center>Centered text</center><br />
__NOTOC__<br />
{| cellspacing="2px" cellpadding="20" border="0" <br />
|valign="top" width=320px style="padding: 5px|<br />
== Team Members ==<br />
=== Instructors === <br />
[[User:dforehand|David Forehand]]<br><br />
<!--[[User:DavidGilbert|David Gilbert]]<br> --><br />
[http://www.brc.dcs.gla.ac.uk/~drg David Gilbert]<br><br />
[[User:GaryGray|Gary Gray]]<br><br />
[[User:gux|Xu Gu]] [[Image:Glasgow_flags_cn.png|China]]<br><br />
[[User:ghamilton1|Graham Hamilton]]<br><br />
[[User:raya|Raya Khanin]] <br> <!-- Raya must register --><br />
[[User:corriecas|David Leader]]<br><br />
[[User:Susanrosser|Susan Rosser]]<br><br />
[[User:EmmaTravis|Emma Travis]]<br><br />
<br />
=== Students ===<br />
[[User:toby|Toby Friend]] [[Image:Glasgow_flags_en.png|England]]<br><br />
[[User:Rach|Rachael Fulton]] [[Image:Glasgow_flags_sc.png|Scotland]]<br><br />
[[User:mojs|Mai-Britt Jensen]] [[Image:Glasgow_flags_dk.png|Denmark]]<br><br />
[[User:0602359k |Karolis Kidykas]] [[Image:Glasgow_flags_lt.png|Lithuania]]<br><br />
[[User:freestym|Martina Marbà]] [[Image:Glasgow_flag_es.png|Spain]]<br><br />
[[User:charkness|Christine Harkness]]<br><br />
[[User:christinemerrick|Christine Merrick]] [[Image:Glasgow_flags_sc.png|Scotland]]<br><br />
[[User:MaijaP|Maija Paakkunainen]] [[Image:Glasgow_flags_fi.png|Finland]]<br><br />
[[User:scott.w.ramsay|Scott Ramsay]] [[Image:Glasgow_flags_sc.png|Scotland]]<br><br />
[[User:mcek|Maciej Trybiło]] [[Image:Glasgow_flags_pl.png|Poland]]<br><br />
[[User:peterz|Petr Znamenskiy]] [[Image:Glasgow_flags_ru.png|Russia]]<br></div>Tobyhttp://2007.igem.org/wiki/index.php/File:Glasgow_team_photo.jpgFile:Glasgow team photo.jpg2007-07-13T15:58:28Z<p>Toby: </p>
<hr />
<div></div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/Meet_the_teamGlasgow/Meet the team2007-07-13T15:54:02Z<p>Toby: </p>
<hr />
<div>[[Image:Team photo.jpg]]<br />
__NOTOC__<br />
{| cellspacing="2px" cellpadding="20" border="0" <br />
|valign="top" width=320px style="padding: 5px|<br />
== Team Members ==<br />
=== Instructors === <br />
[[User:dforehand|David Forehand]]<br><br />
<!--[[User:DavidGilbert|David Gilbert]]<br> --><br />
[http://www.brc.dcs.gla.ac.uk/~drg David Gilbert]<br><br />
[[User:GaryGray|Gary Gray]]<br><br />
[[User:gux|Xu Gu]] [[Image:Glasgow_flags_cn.png|China]]<br><br />
[[User:ghamilton1|Graham Hamilton]]<br><br />
[[User:raya|Raya Khanin]] <br> <!-- Raya must register --><br />
[[User:corriecas|David Leader]]<br><br />
[[User:Susanrosser|Susan Rosser]]<br><br />
[[User:EmmaTravis|Emma Travis]]<br><br />
<br />
=== Students ===<br />
[[User:toby|Toby Friend]] [[Image:Glasgow_flags_en.png|England]]<br><br />
[[User:Rach|Rachael Fulton]] [[Image:Glasgow_flags_sc.png|Scotland]]<br><br />
[[User:mojs|Mai-Britt Jensen]] [[Image:Glasgow_flags_dk.png|Denmark]]<br><br />
[[User:0602359k |Karolis Kidykas]] [[Image:Glasgow_flags_lt.png|Lithuania]]<br><br />
[[User:freestym|Martina Marbà]] [[Image:Glasgow_flag_es.png|Spain]]<br><br />
[[User:charkness|Christine Harkness]]<br><br />
[[User:christinemerrick|Christine Merrick]] [[Image:Glasgow_flags_sc.png|Scotland]]<br><br />
[[User:MaijaP|Maija Paakkunainen]] [[Image:Glasgow_flags_fi.png|Finland]]<br><br />
[[User:scott.w.ramsay|Scott Ramsay]] [[Image:Glasgow_flags_sc.png|Scotland]]<br><br />
[[User:mcek|Maciej Trybiło]] [[Image:Glasgow_flags_pl.png|Poland]]<br><br />
[[User:peterz|Petr Znamenskiy]] [[Image:Glasgow_flags_ru.png|Russia]]<br><br />
<br />
| valign="top" width=320px style="padding: 5px|</div>Tobyhttp://2007.igem.org/wiki/index.php/File:Team_photo.jpgFile:Team photo.jpg2007-07-13T15:50:54Z<p>Toby: </p>
<hr />
<div></div>Tobyhttp://2007.igem.org/wiki/index.php/GlasgowGlasgow2007-07-13T15:42:27Z<p>Toby: </p>
<hr />
<div>[[Image:Glasgow header.png]]<br />
[[Glasgow/Background|BACKGROUND]]<br><br />
[[Glasgow/Plan|PLAN]]<br><br />
[[Glasgow/Meet_the_team|MEET THE TEAM]] [[Glasgow/Drylab|DRYLAB]] [[Glasgow/Wetlab|WETLAB]]<br />
<br />
== Links ==<br />
[http://www.gla.ac.uk Glasgow University] <br><br />
[http://en.wikipedia.org/wiki/Help:Wikitext_examples wiki text examples] <br><br />
[[Glasgow/Diary | Diary]]<br><br />
[[Glasgow/Lectures | Tutorials (understanding each other)]]<br />
<br />
== Goals Of this Project ==<br />
Save the world from lack of energy<br><br />
Detect some bad stuff<br><br />
Have some fun</div>Tobyhttp://2007.igem.org/wiki/index.php/GlasgowGlasgow2007-07-13T15:36:12Z<p>Toby: </p>
<hr />
<div>[[Image:Glasgow header.png]] <br />
[[Glasgow/Meet_the_team|MEET THE TEAM]]<br><br />
<br />
<br />
== Links ==<br />
[http://www.gla.ac.uk Glasgow University] <br><br />
[http://en.wikipedia.org/wiki/Help:Wikitext_examples wiki text examples] <br><br />
[[Glasgow/Diary | Diary]]<br><br />
[[Glasgow/Lectures | Tutorials (understanding each other)]]<br />
<br />
== Goals Of this Project ==<br />
Save the world from lack of energy<br><br />
Detect some bad stuff<br><br />
Have some fun</div>Tobyhttp://2007.igem.org/wiki/index.php/Glasgow/Meet_the_teamGlasgow/Meet the team2007-07-13T15:32:38Z<p>Toby: </p>
<hr />
<div>__NOTOC__<br />
{| cellspacing="2px" cellpadding="20" border="0" <br />
|valign="top" width=320px style="padding: 5px|<br />
== Team Members ==<br />
=== Instructors === <br />
[[User:dforehand|David Forehand]]<br><br />
<!--[[User:DavidGilbert|David Gilbert]]<br> --><br />
[http://www.brc.dcs.gla.ac.uk/~drg David Gilbert]<br><br />
[[User:GaryGray|Gary Gray]]<br><br />
[[User:gux|Xu Gu]] [[Image:Glasgow_flags_cn.png|China]]<br><br />
[[User:ghamilton1|Graham Hamilton]]<br><br />
[[User:raya|Raya Khanin]] <br> <!-- Raya must register --><br />
[[User:corriecas|David Leader]]<br><br />
[[User:Susanrosser|Susan Rosser]]<br><br />
[[User:EmmaTravis|Emma Travis]]<br><br />
<br />
=== Students ===<br />
[[User:toby|Toby Friend]] [[Image:Glasgow_flags_en.png|England]]<br><br />
[[User:Rach|Rachael Fulton]] [[Image:Glasgow_flags_sc.png|Scotland]]<br><br />
[[User:mojs|Mai-Britt Jensen]] [[Image:Glasgow_flags_dk.png|Denmark]]<br><br />
[[User:0602359k |Karolis Kidykas]] [[Image:Glasgow_flags_lt.png|Lithuania]]<br><br />
[[User:freestym|Martina Marbà]] [[Image:Glasgow_flag_es.png|Spain]]<br><br />
[[User:charkness|Christine Harkness]]<br><br />
[[User:christinemerrick|Christine Merrick]] [[Image:Glasgow_flags_sc.png|Scotland]]<br><br />
[[User:MaijaP|Maija Paakkunainen]] [[Image:Glasgow_flags_fi.png|Finland]]<br><br />
[[User:scott.w.ramsay|Scott Ramsay]] [[Image:Glasgow_flags_sc.png|Scotland]]<br><br />
[[User:mcek|Maciej Trybiło]] [[Image:Glasgow_flags_pl.png|Poland]]<br><br />
[[User:peterz|Petr Znamenskiy]] [[Image:Glasgow_flags_ru.png|Russia]]<br><br />
<br />
| valign="top" width=320px style="padding: 5px|</div>Tobyhttp://2007.igem.org/wiki/index.php/GlasgowGlasgow2007-07-13T09:38:28Z<p>Toby: /* Our Goals Of this Project */</p>
<hr />
<div>[[Image:Glasgow header.png]] <br />
<br />
__NOTOC__<br />
{| cellspacing="2px" cellpadding="20" border="0" <br />
|valign="top" width=320px style="padding: 5px|<br />
== Team Members ==<br />
=== Instructors === <br />
[[User:dforehand|David Forehand]]<br><br />
<!--[[User:DavidGilbert|David Gilbert]]<br> --><br />
[http://www.brc.dcs.gla.ac.uk/~drg David Gilbert]<br><br />
[[User:GaryGray|Gary Gray]]<br><br />
[[User:gux|Xu Gu]] [[Image:Glasgow_flags_cn.png|China]]<br><br />
[[User:ghamilton1|Graham Hamilton]]<br><br />
[[User:raya|Raya Khanin]] <br> <!-- Raya must register --><br />
[[User:corriecas|David Leader]]<br><br />
[[User:Susanrosser|Susan Rosser]]<br><br />
[[User:EmmaTravis|Emma Travis]]<br><br />
<br />
=== Students ===<br />
[[User:toby|Toby Friend]] [[Image:Glasgow_flags_en.png|England]]<br><br />
[[User:Rach|Rachael Fulton]] [[Image:Glasgow_flags_sc.png|Scotland]]<br><br />
[[User:mojs|Mai-Britt Jensen]] [[Image:Glasgow_flags_dk.png|Denmark]]<br><br />
[[User:0602359k |Karolis Kidykas]] [[Image:Glasgow_flags_lt.png|Lithuania]]<br><br />
[[User:freestym|Martina Marbà]] [[Image:Glasgow_flag_es.png|Spain]]<br><br />
[[User:charkness|Christine Harkness]]<br><br />
[[User:christinemerrick|Christine Merrick]] [[Image:Glasgow_flags_sc.png|Scotland]]<br><br />
[[User:MaijaP|Maija Paakkunainen]] [[Image:Glasgow_flags_fi.png|Finland]]<br><br />
[[User:scott.w.ramsay|Scott Ramsay]] [[Image:Glasgow_flags_sc.png|Scotland]]<br><br />
[[User:mcek|Maciej Trybiło]] [[Image:Glasgow_flags_pl.png|Poland]]<br><br />
[[User:peterz|Petr Znamenskiy]] [[Image:Glasgow_flags_ru.png|Russia]]<br><br />
<br />
| valign="top" width=320px style="padding: 5px|<br />
<br />
== Links ==<br />
[http://www.gla.ac.uk Glasgow University] <br><br />
[http://en.wikipedia.org/wiki/Help:Wikitext_examples wiki text examples] <br><br />
[[Glasgow/Diary | Diary]]<br><br />
[[Glasgow/Lectures | Lectures]]<br />
<br />
== Goals Of this Project ==<br />
Save the world from lack of energy<br><br />
Detect some bad stuff<br><br />
Have some fun</div>Tobyhttp://2007.igem.org/wiki/index.php/User:TobyUser:Toby2007-07-13T09:19:29Z<p>Toby: </p>
<hr />
<div>[[Image:University_tower.jpg|50x100px|thumb|[http://www.gla.ac.uk Glasgow University Website]]]<br />
'''TOBY THOMAS FRIEND'''<br><br />
<br><br />
I have just finished a degree in Product Design Enghineering, a course which has equipped me with some modelling skills required to aid the iGEM project; I also hope to provide the glasgow iGEM team with some creative flare and product visualisation.<br />
<br />
Next year I am starting a master's course at UCL studying philosophy.<br />
<br />
Email me please, I'm lonely: '''tobusan@gmail.com'''<br />
<br />
[http://www.ebaumsworld.com/games/play/792| click on me for some fun!]<br></div>Tobyhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-11T14:10:40Z<p>Toby: /* RKIP network */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
[[Image:simpledecay.jpg]]<br />
<br />
[[Image:reversible.jpg]]<br />
<br />
[[Image:addition.jpg]]<br />
<br />
[[Image:enzyme.jpg]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG | 700px]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in [[Mass-Action Reaction Modelling]] and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
=== Michaelis-Menton ===<br />
Anybody who has done any sort of biological study will know michaelis menton what i am trying to acheive here is to take it from the basics so as to equate it to the equations we will be using to model the system and to give the biologists an idea of what values and models we need.<br />
The michaelis-Menton equation describes the kinetic properties of many enzymes. Consider the simple system A -> P<br />
The rate of V is the quantity of A that disappears over a specified unit of time which is equal to the rate of appearance of P. For this system V=k[A] where k is the rate constant. <br />
The simplest model that accounts for the kinetic properties of many enzymes is<br />
<br />
=== Sum & And Promoters ===<br />
<br />
=== Application ===</div>Tobyhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-11T14:10:06Z<p>Toby: /* RKIP network */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
[[Image:simpledecay.jpg]]<br />
<br />
[[Image:reversible.jpg]]<br />
<br />
[[Image:addition.jpg]]<br />
<br />
[[Image:enzyme.jpg]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG | 700px]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jp]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in [[Mass-Action Reaction Modelling]] and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
=== Michaelis-Menton ===<br />
Anybody who has done any sort of biological study will know michaelis menton what i am trying to acheive here is to take it from the basics so as to equate it to the equations we will be using to model the system and to give the biologists an idea of what values and models we need.<br />
The michaelis-Menton equation describes the kinetic properties of many enzymes. Consider the simple system A -> P<br />
The rate of V is the quantity of A that disappears over a specified unit of time which is equal to the rate of appearance of P. For this system V=k[A] where k is the rate constant. <br />
The simplest model that accounts for the kinetic properties of many enzymes is<br />
<br />
=== Sum & And Promoters ===<br />
<br />
=== Application ===</div>Tobyhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-11T14:06:56Z<p>Toby: /* Sensitivity */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
[[Image:simpledecay.jpg]]<br />
<br />
[[Image:reversible.jpg]]<br />
<br />
[[Image:addition.jpg]]<br />
<br />
[[Image:enzyme.jpg]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG | 700px]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in [[Mass-Action Reaction Modelling]] and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
=== Michaelis-Menton ===<br />
Anybody who has done any sort of biological study will know michaelis menton what i am trying to acheive here is to take it from the basics so as to equate it to the equations we will be using to model the system and to give the biologists an idea of what values and models we need.<br />
The michaelis-Menton equation describes the kinetic properties of many enzymes. Consider the simple system A -> P<br />
The rate of V is the quantity of A that disappears over a specified unit of time which is equal to the rate of appearance of P. For this system V=k[A] where k is the rate constant. <br />
The simplest model that accounts for the kinetic properties of many enzymes is<br />
<br />
=== Sum & And Promoters ===<br />
<br />
=== Application ===</div>Tobyhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-11T14:06:16Z<p>Toby: /* Sensitivity */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
[[Image:simpledecay.jpg]]<br />
<br />
[[Image:reversible.jpg]]<br />
<br />
[[Image:addition.jpg]]<br />
<br />
[[Image:enzyme.jpg]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG | 700px]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in [[ Mass Action Reaction Modelling]] and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
=== Michaelis-Menton ===<br />
Anybody who has done any sort of biological study will know michaelis menton what i am trying to acheive here is to take it from the basics so as to equate it to the equations we will be using to model the system and to give the biologists an idea of what values and models we need.<br />
The michaelis-Menton equation describes the kinetic properties of many enzymes. Consider the simple system A -> P<br />
The rate of V is the quantity of A that disappears over a specified unit of time which is equal to the rate of appearance of P. For this system V=k[A] where k is the rate constant. <br />
The simplest model that accounts for the kinetic properties of many enzymes is<br />
<br />
=== Sum & And Promoters ===<br />
<br />
=== Application ===</div>Tobyhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-11T14:05:16Z<p>Toby: /* Sensitivity */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
[[Image:simpledecay.jpg]]<br />
<br />
[[Image:reversible.jpg]]<br />
<br />
[[Image:addition.jpg]]<br />
<br />
[[Image:enzyme.jpg]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG | 700px]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in [[Dry to Wet|Mass-Action Reaction]] and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
=== Michaelis-Menton ===<br />
Anybody who has done any sort of biological study will know michaelis menton what i am trying to acheive here is to take it from the basics so as to equate it to the equations we will be using to model the system and to give the biologists an idea of what values and models we need.<br />
The michaelis-Menton equation describes the kinetic properties of many enzymes. Consider the simple system A -> P<br />
The rate of V is the quantity of A that disappears over a specified unit of time which is equal to the rate of appearance of P. For this system V=k[A] where k is the rate constant. <br />
The simplest model that accounts for the kinetic properties of many enzymes is<br />
<br />
=== Sum & And Promoters ===<br />
<br />
=== Application ===</div>Tobyhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-11T14:00:07Z<p>Toby: /* RKIP network */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
[[Image:simpledecay.jpg]]<br />
<br />
[[Image:reversible.jpg]]<br />
<br />
[[Image:addition.jpg]]<br />
<br />
[[Image:enzyme.jpg]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG | 700px]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in..... and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
=== Michaelis-Menton ===<br />
Anybody who has done any sort of biological study will know michaelis menton what i am trying to acheive here is to take it from the basics so as to equate it to the equations we will be using to model the system and to give the biologists an idea of what values and models we need.<br />
The michaelis-Menton equation describes the kinetic properties of many enzymes. Consider the simple system A -> P<br />
The rate of V is the quantity of A that disappears over a specified unit of time which is equal to the rate of appearance of P. For this system V=k[A] where k is the rate constant. <br />
The simplest model that accounts for the kinetic properties of many enzymes is<br />
<br />
=== Sum & And Promoters ===<br />
<br />
=== Application ===</div>Tobyhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-11T13:59:03Z<p>Toby: /* Sensitivity */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
[[Image:simpledecay.jpg]]<br />
<br />
[[Image:reversible.jpg]]<br />
<br />
[[Image:addition.jpg]]<br />
<br />
[[Image:enzyme.jpg]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in..... and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response.jpg | 800px]]<br />
<br />
=== Michaelis-Menton ===<br />
<br />
=== Sum & And Promoters ===<br />
<br />
=== Application ===</div>Tobyhttp://2007.igem.org/wiki/index.php/File:Metabolic_sensetivity_response.jpgFile:Metabolic sensetivity response.jpg2007-07-11T13:53:02Z<p>Toby: </p>
<hr />
<div></div>Tobyhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-11T13:52:16Z<p>Toby: /* Sensitivity */</p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
[[Image:simpledecay.jpg]]<br />
<br />
[[Image:reversible.jpg]]<br />
<br />
[[Image:addition.jpg]]<br />
<br />
[[Image:enzyme.jpg]]<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''<br><br />
<br />
One method of exposing the variation of a model is to program a loop exposing a modelled reaction to increasing values of a chosen constant. This process was followed with the metabolic pathway showing in..... and ploted on a graph showing the response of all 4 species for a set range of varying K2 values from 1 to 10 where 10 is highlighted red.<br><br />
[[Image: metabolic sensetivity response]]<br />
<br />
=== Michaelis-Menton ===<br />
<br />
=== Sum & And Promoters ===<br />
<br />
=== Application ===</div>Tobyhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-11T13:40:48Z<p>Toby: </p>
<hr />
<div>=== Mass-Action Reaction Modelling ===<br />
<br />
=== RKIP network ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Sensitivity ===<br />
''An insight into a system's sensitivity will show how the variation of a model can be apportioned qualitatively or quantitatively to different sources of variation''- <br />
=== Michaelis-Menton ===<br />
<br />
=== Sum & And Promoters ===<br />
<br />
=== Application ===</div>Tobyhttp://2007.igem.org/wiki/index.php/File:RKIP_network_graph.jpgFile:RKIP network graph.jpg2007-07-11T13:30:29Z<p>Toby: </p>
<hr />
<div></div>Tobyhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-11T13:30:17Z<p>Toby: </p>
<hr />
<div>=== Christine's Bit ===<br />
<br />
=== Toby's Bit ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time giving the following graph:<br><br />
[[Image:RKIP network graph.jpg]]<br><br />
<br />
=== Karolis' Bit ===<br />
<br />
=== Rachael's Bit ===<br />
<br />
=== Martina's Bit ===<br />
<br />
=== Maciej's Bit ===</div>Tobyhttp://2007.igem.org/wiki/index.php/File:RKIP_network.JPGFile:RKIP network.JPG2007-07-11T13:28:46Z<p>Toby: </p>
<hr />
<div></div>Tobyhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-11T13:28:36Z<p>Toby: </p>
<hr />
<div>=== Christine's Bit ===<br />
<br />
=== Toby's Bit ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br><br />
[[Image:RKIP network.JPG]]<br><br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time.<br />
<br />
=== Karolis' Bit ===<br />
<br />
=== Rachael's Bit ===<br />
<br />
=== Martina's Bit ===<br />
<br />
=== Maciej's Bit ===</div>Tobyhttp://2007.igem.org/wiki/index.php/File:RKIP_network.jpgFile:RKIP network.jpg2007-07-11T13:25:00Z<p>Toby: </p>
<hr />
<div></div>Tobyhttp://2007.igem.org/wiki/index.php/File:Matlab_logo.jpgFile:Matlab logo.jpg2007-07-11T13:24:04Z<p>Toby: </p>
<hr />
<div></div>Tobyhttp://2007.igem.org/wiki/index.php/Dry_to_WetDry to Wet2007-07-11T13:23:41Z<p>Toby: </p>
<hr />
<div>=== Christine's Bit ===<br />
<br />
=== Toby's Bit ===<br />
After gaining a thorough understanding of methods involved with modeling simple mass-action reactions, we can move on to more complex systems such as the RKIP network.<br />
<br />
In the above diagram, substrates, enzymes and substrate/enzyme complexes are represented by numbered circles, rate constants are represented by numbered squares. By isolating individual species and their direct peripheral species (those being formed from or forming the isolated species) we are able to treat the group as a simple mass-action reaction. A differential equation is then found for each species based on the rate constants and code can be written and a graph plotted showing the trend of all the species’ concentration over time.<br />
<br />
=== Karolis' Bit ===<br />
<br />
=== Rachael's Bit ===<br />
<br />
=== Martina's Bit ===<br />
<br />
=== Maciej's Bit ===</div>Toby