New release 0.7.5 (see details below)


PySCeS CBMPy is a new platform for constraint based modelling and analysis. It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist (metabolites, reactions, compartments) while transparently translating these into the underlying mathematical structures used in advanced analysis (LP's, MILP's).

PySCeS CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods developed specifically for the ecosystem modelling: minimal distance methods, flux minimization and input selection.

To cater for a diverse range of modelling needs PySCeS CBMPy supports user interaction via:

CBMPy fully supports a number of open community standards, SBML Level 3 Core, FBC, Groups as well as OMEX and the creation of COMBINE archives. Models can be read/written in SBML FBC versions 1 and 2 as well as older SBML leve 2 dialects.

Quick/fast install


Windows 64bit

Documentation: reference guide 0.7.4

For more information on the development and use of PySCeS CBMPy feel free to contact me:


Latest news


Downloading PySCeS CBMPy

PySCeS CBMPy Releases
Date Release Downloads
Source (Linux/OS X)
20150519 0.7.5 gzip zip zip exe msi
20150414 0.7.4 gzip zip zip exe msi
20150914 0.7.3 gzip zip exe    msi exe msi
20141202 0.7.0 gzip zip exe    msi exe msi
20140903 0.7.0 (RC2)   zip exe  
PySCeS CBMPy Mariner
Date Release Downloads
Source (Linux/OS X)
20140903 0.6.7   zip exe exe

This software is under active development, release candidates are also made available and the latest bleeding edge code can be found on the CBMPy SVN repository.

Documentation and related material:

PySCeS CBMPy in action

Recon 2

The latest human metabolic reconstruction Recon2 (MODEL1109130000) has been translated into SBML Level 3 with FBC extension and is available below. Also available is a CBMPy (0.6.7) generated spreadsheet containing model information, FBA and FVA results. Note that in the translation the objective function has been set as "R_biomass_reaction". Details on the model translation and analysis in CBMPy are available here.

SBML Level 3 with FBC Models for use with CBMPy
Model SBML Level 3 with FBC
SBML file (zipped)
Model information
Excel 97 file (zipped)
MODEL1109130000 (Recon2)

Using CBMPy (0.6.7), FBA is virtually instantaneous and FVA takes about an hour using using 2 threads in multicore mode with CPLEX on an Intel quad core laptop. Please note that other than basic syntax checks no in depth checking has been done to validate the correctness of the translations or results presented here.

PySCeS CBMPy is developed by

Brett Olivier      vu_logo nwo_logo


PySCeS CBMPy is developed under the GNU GPL version 3 as Open Source software. Disclaimer: this software is under active development and is provided as is. Please read the licence the disclaimer provided with the source code for details.