User:Jarle Pahr/Modelling

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Virtual Cell:

COBRA Toolbox - Open source modelling and simulation resources:


Biomodels database:

Models repositories links from

JWS Online model database:

GSMNDB: Genome-Scale Metabolic Network DataBase:

Models of note

Repressilator model:

Research groups

Model generation

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database.:


Pathway Tools:

Reconstructing genome-scale metabolic models with Merlin:


Minimum information requested in the annotation of biochemical models (MIRIAM):

The Effect of Transcription and Translation Initiation Frequencies on the Stochastic Fluctuations in Prokaryotic Gene Expression:

Simulation of genetic circuits:

WholeCellKB: model organism databases for comprehensive whole-cell models:

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli:

Dynamic Modeling of Cellular Populations within iBioSim:

Towards a whole-cell modeling approach for synthetic biology:

A Whole-Cell Computational Model Predicts Phenotype from Genotype:

Integrating Metabolic, Transcriptional Regulatory, and Signal Transduction Models in Escherichia Coli. Bioinformatics. 24(18):2044-2050 (2008)


Biological Modeling and Simulation: A Survey of Practical Models, Algorithms, and Numerical Methods.