Team:Groningen/Brainstorm/Modelling

From 2009.igem.org

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**[https://2008.igem.org/Team:University_of_Washington/Modeling Washington 2008], using Mathematica
**[https://2008.igem.org/Team:University_of_Washington/Modeling Washington 2008], using Mathematica
**[https://2008.igem.org/PHA_Project_Modeling Tsinghua 2008], using Matlab
**[https://2008.igem.org/PHA_Project_Modeling Tsinghua 2008], using Matlab
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**[https://2008.igem.org/Team:BCCS-Bristol/Modeling-GRN BCCS-Bristol 2008], Matlab
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**[https://2008.igem.org/Team:Groningen/modeling_SingleCell.html Groningen 2008!], using Matlab and some custom tools to construct the models
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**[https://2008.igem.org/Team:KULeuven/Model/Overview KULeuven], using Matlab and Celldesigner, site done very decently
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**[https://2008.igem.org/Team:Montreal/Modeling Montreal], using Mathematica
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**[https://2008.igem.org/Team:Paris/Analysis Paris 2008], using BIOCHAM
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**[https://2008.igem.org/Team:UCSF/Modeling UCSF], using Matlab, [[User:Kbover|Klaas Bernd]]: perhaps for growth stages?
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**[https://2008.igem.org/Team:Cambridge/Modelling Cambridge], using an unspecified tool
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**[https://2008.igem.org/Team:Imperial_College/Dry_Lab Imperial College Londen], using Matlab
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**[https://2008.igem.org/Team:Peking_University/Modeling Peking], using Symbiology
*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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**[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?
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*'''NEED TO MERGE'''
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*Group behaviour
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**Gene Regulatory Networks (GRNs)
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**[https://2008.igem.org/Team:BCCS-Bristol/Modeling-Agent_Based BCCS-Bristol 2008], movement of groups of cells, using a home-grown Java tool
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***[https://2008.igem.org/Team:BCCS-Bristol/Modeling-GRN BCCS-Bristol 2008]
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**[https://2008.igem.org/Team:Groningen/modeling_Spatial.html Groningen 2008!], spatial interaction
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**Stochastic Agent Based Simulation
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**[https://2008.igem.org/Team:Heidelberg/Modeling Heidelberg], two population distributions and some substance concentrations using custom Matlab code
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***[https://2008.igem.org/Team:BCCS-Bristol/Modeling-Agent_Based BCCS-Bristol 2008]
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**[https://2008.igem.org/Team:Montreal/Modeling Montreal], interaction in Repressilator network, using Mathematica
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**Hybrid Model (BSim v2)
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**[https://2008.igem.org/Team:Cambridge/Modelling#Modelling_the_complete_agr-quorum_sensing_system Cambridge], quorum sensing
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***[https://2008.igem.org/Team:BCCS-Bristol/Modeling-Hybrid BCCS-Bristol 2008]
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**[https://2008.igem.org/Team:Imperial_College/Dry_Lab Imperial College Londen], growth curve and motility, using Matlab
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**Genetic Network Generating Spatial Patterns Through Cell-Cell Communication and Controlled Information Processing
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*Mutation
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***[https://2008.igem.org/Team:EPF-Lausanne/Modeling EPF-Lausanne], need to find exactly what they did.
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**[https://2008.igem.org/Team:Peking_University/Modeling Peking]
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**Conways game of life
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***[https://2008.igem.org/Team:Groningen/modeling_SingleCell.html Groningen!], singel cell
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***[https://2008.igem.org/Team:Groningen/modeling_Spatial.html Groningen], spatial approach
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***[https://2008.igem.org/Team:Groningen/modeling_files.html Groningen], modeling files
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**Ecolicence to kill: Engineering E.coli for targeting pathogenic microorganisms
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***[https://2008.igem.org/Team:Heidelberg/Modeling Heidelberg]
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**Dr. Coli, the bacterial drug delivery system
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***[https://2008.igem.org/Team:KULeuven/Model/Overview KULeuven], done very decently
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**Occilations in large numbers of cells
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***[https://2008.igem.org/Team:Montreal/Modeling Montreal], done in mathematica, serveral years of research
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**Bacterial Clock
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***[https://2008.igem.org/Team:Paris/Construction Paris], see how this fits in one of our projects
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**Cellular Memory
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***[https://2008.igem.org/Team:UCSF/Modeling UCSF], perhaps for growth stages?
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**Quorum sensing
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***[https://2008.igem.org/Team:Cambridge/Modelling#Modelling_the_complete_agr-quorum_sensing_system Cambridge], Perhaps for growth stages?
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**Light sensing
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***[https://2008.igem.org/Team:Imperial_College/Dry_Lab Imperial College Londen], mayby for one of our projects.
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**The floating Bacteria
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***[https://2008.igem.org/Team:Kyoto/Project Kyoto], lets have a very good look at what these guys have been doing
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**Genetic Cricuit
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***[https://2008.igem.org/Team:Peking_University/Modeling Peking]
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Other potentially interesting software tools:
Other potentially interesting software tools:
*[https://2008.igem.org/Team:UC_Berkeley_Tools UC Berkeley's Clotho]
*[https://2008.igem.org/Team:UC_Berkeley_Tools UC Berkeley's Clotho]
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*SBML?
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*SBML? (language to specify models)
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*[https://2008.igem.org/Team:KULeuven/Software/Simbiology2LaTeX KU Leuven's Simbiology2LaTeX]
==Literature==
==Literature==
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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 [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).
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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 [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) and 610A (and possibly 625, 715).

Revision as of 13:18, 27 April 2009

Home The Team Brainstorm Our Vision Parts Modelling Notebook


Software tools from previous years

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), as well as 605C/D/E (A and Z also exist but seem to be less interesting) and 610A (and possibly 625, 715).