Team:Groningen/Brainstorm/Modelling

From 2009.igem.org

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==Systems from previous years==
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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)
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*Molecular/genetic Circuit (?)
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*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]
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**(?)[https://2008.igem.org/Team:Istanbul/Modeling Istanbul 2008], using the Symbiology toolbox
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**[https://2008.igem.org/Team:LCG-UNAM-Mexico/Modeling LCG-UNAM-Mexico 2008], using the Symbiology toolbox
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**[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)
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**[https://2008.igem.org/Team:Purdue/Modeling Purdue 2008], using Excel and Mathcad
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**[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
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**[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?)
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Other potentially interesting software tools:
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*[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
  • Cell processes
    • Calgary 2008, using their own tool (transcription and translation)
  • Static genome analysis (?)
  • Genome Scale Model (whole cell response)
    • ETH Zurich 2008, using the [http://gcrg.ucsd.edu/Downloads/Cobra_Toolbox Cobra Toolbox] for Matlab
  • Chemostat simulation
  • Cell movement

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).