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Team:University of Sheffield /Misc
From 2008.igem.org
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[[media:University_of_Sheffield_iGEM_Presentation_to_Chelsi.ppt|Presentation as a Microsoft PowerPoint file]] | [[media:University_of_Sheffield_iGEM_Presentation_to_Chelsi.ppt|Presentation as a Microsoft PowerPoint file]] | ||
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==Software== | ==Software== | ||
| + | |||
| + | ===Dropbox=== | ||
[[Image:Dropbox_logo.png|250px|right|Dropbox logo]] | [[Image:Dropbox_logo.png|250px|right|Dropbox logo]] | ||
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[https://www.getdropbox.com/ Dropbox homepage] | [https://www.getdropbox.com/ Dropbox homepage] | ||
| + | |||
| + | ---- | ||
| + | |||
| + | ===Matlab=== | ||
| + | |||
| + | [[Image:Matlab_logo.png|90px|right|MatLab logo]] | ||
| + | |||
| + | Modelling stages mostly used MatLab. Your university should be able to provide this somewhere, as it's expensive but very useful. | ||
| + | |||
| + | [http://www.mathworks.com/ MatLab homepage] | ||
| + | |||
| + | |||
---- | ---- | ||
| + | |||
| + | ===Utopia=== | ||
| + | |||
| + | [[Image:Utopia software.jpg|200px|right|Utopia logo]] | ||
| + | |||
| + | Utopia is a collection of interactive tools for analysing protein sequence and structure. Up front are user-friendly and responsive visualisation applications, behind the scenes a sophisticated model that allows these to work together and hides much of the tedious work of dealing with file formats and web services. | ||
| + | |||
| + | [http://utopia.cs.manchester.ac.uk/ Utopia homepage] | ||
| + | |||
| + | ---- | ||
| + | |||
| + | ===Clone Manager=== | ||
| + | |||
| + | [[Image:Clone_manager.jpg|200px|right|Clone manager]] | ||
| + | |||
| + | Clone Manager is an expert system to help with cloning simulation, enzyme operations and graphic map drawing. It can be also used as a quick and easy way to view or edit sequence files, find open reading frames, translate genes, or find genes or text in files. | ||
| + | |||
| + | [http://www.scied.com/pr_cmbas.htm Clone Manager homepage] | ||
| + | |||
| + | ===Matlab codes=== | ||
| + | function xdot=iGEM2(t,x) | ||
| + | k1=0.0029; | ||
| + | k_1=0.00088; | ||
| + | k2=108; | ||
| + | k_2=1080; | ||
| + | k3=90; | ||
| + | kb=5400; | ||
| + | k_b=360; | ||
| + | ATP=100; | ||
| + | ADP=8; | ||
| + | |||
| + | a = -k_1*x(1)*ADP - k2*x(1)*0.5*(4-x(3)-x(2)) + k1*(1-x(1))*ATP + k_2*(1-x(1))*x(2); | ||
| + | |||
| + | b = -k_2*(1-x(1))*x(2) - k3*x(2)*(1-x(1)) -2*kb*x(2)*x(2)*(100-x(3)) + k2*x(1)*0.5*(4-x(3)-x(2)) + k_b*x(3); | ||
| + | |||
| + | c = -k_b*x(3) + 2*kb*x(2)*x(2)*(100-x(3)); | ||
| + | |||
| + | xdot=[a;b;c]; | ||
| + | |||
| + | |||
| + | All units in µM | ||
| + | |||
| + | t0=0; | ||
| + | tf=5; | ||
| + | tspan=[t0:tf]; | ||
| + | x_initial=[0;0;0]; | ||
| + | [t,x]=ode45(@iGEM2,tspan,x_initial); | ||
==Links== | ==Links== | ||
Latest revision as of 11:56, 29 October 2008
| Introduction | Our project | Modelling | Wet Lab | Our team | Timetable | Miscellaneous |
|---|
Contents |
Presentations
You can download a presentation we gave to some of our sponsors summarizing our project here:
Presentation as a Microsoft PowerPoint file
Software
Dropbox
Highly recommended!!
DROPBOX is a brillaint way to share information as a team without constant emails and attachments. Everyone downloads the program, and shares a single account. Then drag and drop any files you want the team to see/have updated into the 'box' on your desktop, and everyone gets a small windows popup telling them which files have changed when they connect to the internet. We found this completely invaluable for both assigning papers to read and when all editing group work togther (such as our funding proposal)
Matlab
Modelling stages mostly used MatLab. Your university should be able to provide this somewhere, as it's expensive but very useful.
[http://www.mathworks.com/ MatLab homepage]
Utopia
Utopia is a collection of interactive tools for analysing protein sequence and structure. Up front are user-friendly and responsive visualisation applications, behind the scenes a sophisticated model that allows these to work together and hides much of the tedious work of dealing with file formats and web services.
[http://utopia.cs.manchester.ac.uk/ Utopia homepage]
Clone Manager
Clone Manager is an expert system to help with cloning simulation, enzyme operations and graphic map drawing. It can be also used as a quick and easy way to view or edit sequence files, find open reading frames, translate genes, or find genes or text in files.
[http://www.scied.com/pr_cmbas.htm Clone Manager homepage]
Matlab codes
function xdot=iGEM2(t,x) k1=0.0029; k_1=0.00088; k2=108; k_2=1080; k3=90; kb=5400; k_b=360; ATP=100; ADP=8;
a = -k_1*x(1)*ADP - k2*x(1)*0.5*(4-x(3)-x(2)) + k1*(1-x(1))*ATP + k_2*(1-x(1))*x(2);
b = -k_2*(1-x(1))*x(2) - k3*x(2)*(1-x(1)) -2*kb*x(2)*x(2)*(100-x(3)) + k2*x(1)*0.5*(4-x(3)-x(2)) + k_b*x(3);
c = -k_b*x(3) + 2*kb*x(2)*x(2)*(100-x(3));
xdot=[a;b;c];
All units in µM
t0=0; tf=5; tspan=[t0:tf]; x_initial=[0;0;0]; [t,x]=ode45(@iGEM2,tspan,x_initial);
