Software & Resources

Software

Our Internal Software Projects

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

Other Parameter Estimation Packages

PESTO, parameter estimation toolbox:

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

PyABC: ICB-DCM/pyABC

writing and Editing of sbml models

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

Visualisation

1. iVUN, a systems biology network visualisation tool

Web-based tools

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