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Team:Groningen/Brainstorm/Modelling
From 2009.igem.org
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| - | == | + | ==Software tools from previous years== |
*RNA folding (secondary structure) | *RNA folding (secondary structure) | ||
**[https://2008.igem.org/Team:Alberta_NINT/Modeling Alberta 2008], using [http://rna.urmc.rochester.edu/rnastructure.html RNAstructure] and UNAFold (with a front-end), they used both programs (presumably to get an idea of the certainty) | **[https://2008.igem.org/Team:Alberta_NINT/Modeling Alberta 2008], using [http://rna.urmc.rochester.edu/rnastructure.html RNAstructure] and UNAFold (with a front-end), they used both programs (presumably to get an idea of the certainty) | ||
| - | *Molecular/genetic Circuit (?) | + | *Molecular/genetic Circuit (?), (small) systems of (non-linear) ODEs |
**[https://2008.igem.org/Team:Bologna/Modeling Bologna 2008], using Simulink (Mathworks) | **[https://2008.igem.org/Team:Bologna/Modeling Bologna 2008], using Simulink (Mathworks) | ||
**[https://2008.igem.org/Team:ETH_Zurich/Modeling/Switch_Circuit ETH Zurich 2008], using the Symbiology toolbox in Matlab | **[https://2008.igem.org/Team:ETH_Zurich/Modeling/Switch_Circuit ETH Zurich 2008], using the Symbiology toolbox in Matlab | ||
**[https://2008.igem.org/Team:iHKU/modeling IHKU 2008] | **[https://2008.igem.org/Team:iHKU/modeling IHKU 2008] | ||
| + | **(?)[https://2008.igem.org/Team:Istanbul/Modeling Istanbul 2008], using the Symbiology toolbox | ||
| + | **[https://2008.igem.org/Team:LCG-UNAM-Mexico/Modeling LCG-UNAM-Mexico 2008], using the Symbiology toolbox | ||
| + | **[https://2008.igem.org/Team:NTU-Singapore/Modelling/Deterministic_Modeling NTU Singapore 2008], using Simulink, [http://www.sbtoolbox2.org/main.php Systems Biology Toolbox 2] (sensitivity analysis) and [http://www.cellware.org/index.html CellWare] (stochastic analysis) | ||
| + | **[https://2008.igem.org/Team:Purdue/Modeling Purdue 2008], using Excel and Mathcad | ||
| + | **[https://2008.igem.org/Team:TUDelft/Color_modeling TU Delft 2008], using CellDesigner and the [http://www.sys-bio.org/ Synthetic Biology Workbench] for Matlab | ||
*Cell processes | *Cell processes | ||
**[https://2008.igem.org/Modeling Calgary 2008], using their own tool (transcription and translation) | **[https://2008.igem.org/Modeling Calgary 2008], using their own tool (transcription and translation) | ||
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*Cell movement | *Cell movement | ||
**[https://2008.igem.org/Team:iHKU/modeling IHKU 2008], as random walks | **[https://2008.igem.org/Team:iHKU/modeling IHKU 2008], as random walks | ||
| + | **[https://2008.igem.org/Team:University_of_Lethbridge/Modeling University of Lethbridge 2008], using [http://www.pdn.cam.ac.uk/groups/comp-cell/BCT.html BCT] (a tool to model the chemotaxis pathway of E. Coli?) | ||
| + | |||
| + | Other potentially interesting software tools: | ||
| + | *[https://2008.igem.org/Team:UC_Berkeley_Tools UC Berkeley's Clotho] | ||
==Literature== | ==Literature== | ||
See our [[Team:Groningen/Literature/Modelling|literature list]]. For our team members that are looking for books on the subject, have a look under code 605B (Bernoulliborg library, lower floor). | See our [[Team:Groningen/Literature/Modelling|literature list]]. For our team members that are looking for books on the subject, have a look under code 605B (Bernoulliborg library, lower floor). | ||
Revision as of 10:14, 22 April 2009
Software tools from previous years
- RNA folding (secondary structure)
- Alberta 2008, using [http://rna.urmc.rochester.edu/rnastructure.html RNAstructure] and UNAFold (with a front-end), they used both programs (presumably to get an idea of the certainty)
- Molecular/genetic Circuit (?), (small) systems of (non-linear) ODEs
- Bologna 2008, using Simulink (Mathworks)
- ETH Zurich 2008, using the Symbiology toolbox in Matlab
- IHKU 2008
- (?)Istanbul 2008, using the Symbiology toolbox
- LCG-UNAM-Mexico 2008, using the Symbiology toolbox
- NTU Singapore 2008, using Simulink, [http://www.sbtoolbox2.org/main.php Systems Biology Toolbox 2] (sensitivity analysis) and [http://www.cellware.org/index.html CellWare] (stochastic analysis)
- Purdue 2008, using Excel and Mathcad
- TU Delft 2008, using CellDesigner and the [http://www.sys-bio.org/ Synthetic Biology Workbench] for Matlab
- Cell processes
- Calgary 2008, using their own tool (transcription and translation)
- Static genome analysis (?)
- ETH Zurich 2008, using their own tool
- Genome Scale Model (whole cell response)
- ETH Zurich 2008, using the [http://gcrg.ucsd.edu/Downloads/Cobra_Toolbox Cobra Toolbox] for Matlab
- Chemostat simulation
- ETH Zurich 2008, using their genome scale model data
- Cell movement
- IHKU 2008, as random walks
- University of Lethbridge 2008, using [http://www.pdn.cam.ac.uk/groups/comp-cell/BCT.html BCT] (a tool to model the chemotaxis pathway of E. Coli?)
Other potentially interesting software tools:
Literature
See our literature list. For our team members that are looking for books on the subject, have a look under code 605B (Bernoulliborg library, lower floor).
