User:Jarle Pahr/Modelling: Difference between revisions
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Dynamic Modeling of Cellular Populations within iBioSim: http://pubs.acs.org/doi/abs/10.1021/sb300082b | Dynamic Modeling of Cellular Populations within iBioSim: http://pubs.acs.org/doi/abs/10.1021/sb300082b | ||
Towards a whole-cell modeling approach for synthetic biology: http:// | Towards a whole-cell modeling approach for synthetic biology: http://chaos.aip.org/resource/1/chaoeh/v23/i2/p025112_s1?isAuthorized=no | ||
Revision as of 13:59, 6 July 2013
Openworm
http://www.youtube.com/watch?v=DIb_Z7QkmIA
Software
COBRA Toolbox
http://derkje-j.github.io/programming-life/
Simtk.org - Open source modelling and simulation resources: https://simtk.org/xml/index.xml
Databases
Biomodels database: http://biomodels.caltech.edu/
Models repositories links from systems-biology.org: http://systems-biology.org/resources/model-repositories/
JWS Online model database: http://jjj.biochem.sun.ac.za/database/index.html
GSMNDB: Genome-Scale Metabolic Network DataBase: http://synbio.tju.edu.cn/GSMNDB/gsmndb.htm
Research groups
http://covertlab.stanford.edu/
Model generation
MicrobesFlux: a web platform for drafting metabolic models from the KEGG database.: http://www.ncbi.nlm.nih.gov/pubmed/22857267
http://tanglab.engineering.wustl.edu/static/MicrobesFlux.html
Path2models: http://code.google.com/p/path2models/
Pathway Tools: http://bib.oxfordjournals.org/content/11/1/40
Reconstructing genome-scale metabolic models with Merlin: http://academia.edu/2841218/Reconstructing_genome-scale_metabolic_models_with_Merlin
Bibliography
WholeCellKB: model organism databases for comprehensive whole-cell models: http://nar.oxfordjournals.org/content/early/2012/11/21/nar.gks1108.full
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli: http://bioinformatics.oxfordjournals.org/content/24/18/2044.short
Dynamic Modeling of Cellular Populations within iBioSim: http://pubs.acs.org/doi/abs/10.1021/sb300082b
Towards a whole-cell modeling approach for synthetic biology: http://chaos.aip.org/resource/1/chaoeh/v23/i2/p025112_s1?isAuthorized=no
A Whole-Cell Computational Model Predicts Phenotype from Genotype: http://www.cell.com/abstract/S0092-8674%2812%2900776-3
Integrating Metabolic, Transcriptional Regulatory, and Signal Transduction Models in Escherichia Coli. Bioinformatics. 24(18):2044-2050 (2008)
Books:
Biological Modeling and Simulation: A Survey of Practical Models, Algorithms, and Numerical Methods. http://mitpress.mit.edu/books/biological-modeling-and-simulation
