User:Jarle Pahr/Modelling

Openworm

http://www.openworm.org/

http://www.youtube.com/watch?v=DIb_Z7QkmIA

Software

Virtual Cell: http://vcell.org/vcell_software/login.html

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

Models of note

Repressilator model: http://www.ebi.ac.uk/biomodels-main/BIOMD0000000012

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

http://www.merlin-sysbio.org/

Bibliography

Minimum information requested in the annotation of biochemical models (MIRIAM): http://www.nature.com/nbt/journal/v23/n12/abs/nbt1156.html

The Effect of Transcription and Translation Initiation Frequencies on the Stochastic Fluctuations in Prokaryotic Gene Expression: http://www.jbc.org/content/276/11/8165.short

Simulation of genetic circuits: http://www.annualreviews.org/doi/pdf/10.1146/annurev.biophys.27.1.199

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