Team:Groningen/Brainstorm/Modelling

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Revision as of 13:18, 27 April 2009

Home	The Team	Brainstorm	Our Vision	Parts	Modelling	Notebook

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
- BCCS-Bristol 2008, Matlab
- Groningen 2008!, using Matlab and some custom tools to construct the models
- KULeuven, using Matlab and Celldesigner, site done very decently
- Montreal, using Mathematica
- Paris 2008, using BIOCHAM
- UCSF, using Matlab, Klaas Bernd: perhaps for growth stages?
- Cambridge, using an unspecified tool
- Imperial College Londen, using Matlab
- Peking, using Symbiology
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?
Group behaviour
- BCCS-Bristol 2008, movement of groups of cells, using a home-grown Java tool
- Groningen 2008!, spatial interaction
- Heidelberg, two population distributions and some substance concentrations using custom Matlab code
- Montreal, interaction in Repressilator network, using Mathematica
- Cambridge, quorum sensing
- Imperial College Londen, growth curve and motility, using Matlab
Mutation
- Peking

Other potentially interesting software tools:

UC Berkeley's Clotho
SBML? (language to specify models)
KU Leuven's Simbiology2LaTeX

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) and 610A (and possibly 625, 715).

@@ Line 32: / Line 32: @@
 **[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/Team:BCCS-Bristol/Modeling-GRN BCCS-Bristol 2008], Matlab
+**[https://2008.igem.org/Team:Groningen/modeling_SingleCell.html Groningen 2008!], using Matlab and some custom tools to construct the models
+**[https://2008.igem.org/Team:KULeuven/Model/Overview KULeuven], using Matlab and Celldesigner, site done very decently
+**[https://2008.igem.org/Team:Montreal/Modeling Montreal], using Mathematica
+**[https://2008.igem.org/Team:Paris/Analysis Paris 2008], using BIOCHAM
+**[https://2008.igem.org/Team:UCSF/Modeling UCSF], using Matlab, [[User:Kbover|Klaas Bernd]]: perhaps for growth stages?
+**[https://2008.igem.org/Team:Cambridge/Modelling Cambridge], using an unspecified tool
+**[https://2008.igem.org/Team:Imperial_College/Dry_Lab Imperial College Londen], using Matlab
+**[https://2008.igem.org/Team:Peking_University/Modeling Peking], using Symbiology
 *Cell processes
 **[https://2008.igem.org/Modeling Calgary 2008], using their own tool (transcription and translation)
@@ Line 46: / Line 55: @@
 **[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?
-*'''NEED TO MERGE'''
+*Group behaviour
-**Gene Regulatory Networks (GRNs)
+**[https://2008.igem.org/Team:BCCS-Bristol/Modeling-Agent_Based BCCS-Bristol 2008], movement of groups of cells, using a home-grown Java tool
-***[https://2008.igem.org/Team:BCCS-Bristol/Modeling-GRN BCCS-Bristol 2008]
+**[https://2008.igem.org/Team:Groningen/modeling_Spatial.html Groningen 2008!], spatial interaction
-**Stochastic Agent Based Simulation
+**[https://2008.igem.org/Team:Heidelberg/Modeling Heidelberg], two population distributions and some substance concentrations using custom Matlab code
-***[https://2008.igem.org/Team:BCCS-Bristol/Modeling-Agent_Based BCCS-Bristol 2008]
+**[https://2008.igem.org/Team:Montreal/Modeling Montreal], interaction in Repressilator network, using Mathematica
-**Hybrid Model (BSim v2)
+**[https://2008.igem.org/Team:Cambridge/Modelling#Modelling_the_complete_agr-quorum_sensing_system Cambridge], quorum sensing
-***[https://2008.igem.org/Team:BCCS-Bristol/Modeling-Hybrid BCCS-Bristol 2008]
+**[https://2008.igem.org/Team:Imperial_College/Dry_Lab Imperial College Londen], growth curve and motility, using Matlab
-**Genetic Network Generating Spatial Patterns Through Cell-Cell Communication and Controlled Information Processing
+*Mutation
-***[https://2008.igem.org/Team:EPF-Lausanne/Modeling EPF-Lausanne], need to find exactly what they did.
+**[https://2008.igem.org/Team:Peking_University/Modeling Peking]
-**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:
 *[https://2008.igem.org/Team:UC_Berkeley_Tools UC Berkeley's Clotho]
-*SBML?
+*SBML? (language to specify models)
+*[https://2008.igem.org/Team:KULeuven/Software/Simbiology2LaTeX KU Leuven's Simbiology2LaTeX]
 ==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 [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).
+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).