Software & Resources

Software

Our Internal Software Projects

Markov chain Monte Carlo for use on clusters (MPI and OpenMP): MCMC_CLIB.
ABC uncertainty quantification: UQSA.
R script to convert SBtab files to vfgen: SBtabVFGEN.

Other Parameter Estimation Packages

PESTO, parameter estimation toolbox:

For matlab: ICB-DCM/PESTO.
For Python: ICB-DCM/pyPESTO

PyABC: ICB-DCM/pyABC

writing and Editing of sbml models

Copasi, a GUI Software that supports sbml
SimBiology, a matlab toolbox to create models and export to sbml
SBToolbox2, another matlab toolbox for systems biology
IQM Tools, next version of SBToolbox2

Visualisation

iVUN, a systems biology network visualisation tool

Web-based tools

SBtab, an extensible table format that can be converted into sbml online

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