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Team:Groningen/Brainstorm/Modelling
From 2009.igem.org
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**[https://2008.igem.org/Team:University_of_Lethbridge/Modeling 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?) | **[https://2008.igem.org/Team:University_of_Lethbridge/Modeling 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?) | ||
**[https://2008.igem.org/Chemotaxis_Modeling Tsinghua 2008], using their own code? | **[https://2008.igem.org/Chemotaxis_Modeling Tsinghua 2008], using their own code? | ||
| + | *'''NEED TO MERGE''' | ||
| + | **Gene Regulatory Networks (GRNs) | ||
| + | ***[https://2008.igem.org/Team:BCCS-Bristol/Modeling-GRN BCCS-Bristol 2008] | ||
| + | **Stochastic Agent Based Simulation | ||
| + | ***[https://2008.igem.org/Team:BCCS-Bristol/Modeling-Agent_Based BCCS-Bristol 2008] | ||
| + | **Hybrid Model (BSim v2) | ||
| + | ***[https://2008.igem.org/Team:BCCS-Bristol/Modeling-Hybrid BCCS-Bristol 2008] | ||
| + | **Genetic Network Generating Spatial Patterns Through Cell-Cell Communication and Controlled Information Processing | ||
| + | ***[https://2008.igem.org/Team:EPF-Lausanne/Modeling EPF-Lausanne], need to find exactly what they did. | ||
| + | **Conways game of life | ||
| + | ***[https://2008.igem.org/Team:Groningen/modeling_SingleCell.html Groningen!], singel cell | ||
| + | ***[https://2008.igem.org/Team:Groningen/modeling_Spatial.html Groningen], spatial approach | ||
| + | ***[https://2008.igem.org/Team:Groningen/modeling_files.html Groningen], modeling files | ||
| + | **Ecolicence to kill: Engineering E.coli for targeting pathogenic microorganisms | ||
| + | ***[https://2008.igem.org/Team:Heidelberg/Modeling Heidelberg] | ||
| + | **Dr. Coli, the bacterial drug delivery system | ||
| + | ***[https://2008.igem.org/Team:KULeuven/Model/Overview KULeuven], done very decently | ||
| + | **Occilations in large numbers of cells | ||
| + | ***[https://2008.igem.org/Team:Montreal/Modeling Montreal], done in mathematica, serveral years of research | ||
| + | **Bacterial Clock | ||
| + | ***[https://2008.igem.org/Team:Paris/Construction Paris], see how this fits in one of our projects | ||
| + | **Cellular Memory | ||
| + | ***[https://2008.igem.org/Team:UCSF/Modeling UCSF], perhaps for growth stages? | ||
| + | **Quorum sensing | ||
| + | ***[https://2008.igem.org/Team:Cambridge/Modelling#Modelling_the_complete_agr-quorum_sensing_system Cambridge], Perhaps for growth stages? | ||
| + | **Light sensing | ||
| + | ***[https://2008.igem.org/Team:Imperial_College/Dry_Lab Imperial College Londen], mayby for one of our projects. | ||
| + | **The floating Bacteria | ||
| + | ***[https://2008.igem.org/Team:Kyoto/Project Kyoto], lets have a very good look at what these guys have been doing | ||
| + | **Genetic Cricuit | ||
| + | ***[https://2008.igem.org/Team:Peking_University/Modeling Peking] | ||
Other potentially interesting software tools: | Other potentially interesting software tools: | ||
Revision as of 11:13, 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
- Edinburgh 2008, using [http://www.copasi.org/tiki-index.php COPASI]
- Freiburg 2008, using Matlab
- Johns Hopkins 2008, using Matlab (for population dynamics of yeast)
- Michigan 2008, using Mathematica
- Pavia 2008, using Matlab and Simulink
- Ottawa 2008, using Matlab
- Washington 2008, using Mathematica
- Tsinghua 2008, using Matlab
- Cell processes
- Calgary 2008, using their own tool (transcription and translation)
- Waterloo 2008, using [http://theileria.ccb.sickkids.ca/CellSim/overview.php Cell++]
- 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
- ?Wisconsin 2008, using GAMS
- Chemostat simulation
- ETH Zurich 2008, using their genome scale model data
- Cell movement
- IHKU 2008, as random walks
- 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?)
- Tsinghua 2008, using their own code?
- NEED TO MERGE
- Gene Regulatory Networks (GRNs)
- Stochastic Agent Based Simulation
- Hybrid Model (BSim v2)
- Genetic Network Generating Spatial Patterns Through Cell-Cell Communication and Controlled Information Processing
- EPF-Lausanne, need to find exactly what they did.
- Conways game of life
- Groningen!, singel cell
- Groningen, spatial approach
- Groningen, modeling files
- Ecolicence to kill: Engineering E.coli for targeting pathogenic microorganisms
- Dr. Coli, the bacterial drug delivery system
- KULeuven, done very decently
- Occilations in large numbers of cells
- Montreal, done in mathematica, serveral years of research
- Bacterial Clock
- Paris, see how this fits in one of our projects
- Cellular Memory
- UCSF, perhaps for growth stages?
- Quorum sensing
- Cambridge, Perhaps for growth stages?
- Light sensing
- Imperial College Londen, mayby for one of our projects.
- The floating Bacteria
- Kyoto, lets have a very good look at what these guys have been doing
- Genetic Cricuit
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 [http://opc.ub.rug.nl/DB=1/SET=2/TTL=1/CLK?IKT=8110&TRM=605B 605B] (Bernoulliborg library, lower floor), as well as 605C/D/E (A and Z also exist but seem to be less interesting).
