PySCeS

 

A flexible, user friendly tool for the analysis of cellular systems

 

PySCeS CBMPy is a 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).

The latest CBMPy release is version 0.8.8 (November 2023 ).

CBMPy is build with Python 3.10 and includes support for
SBML3 FBC version 3, QP problems and user defined constraints      

Core CBMPy

  • CBMPy provides a core model data structure that enables model creation editing and analysis without any solver.
  •  This includes: element and charge balancing, network analysis and model validation.
  •  An interactive console, scripting for advanced use or as a library for software development
  • CBMPy has extensive support for mode and component metadata, including MIRIAM annotations, SBO and user-defined key:vaue pairs.
  • CBMPy supports open community standards for model exchange SBML Level 3 Core, FBC, Groups and archiving (SEDML, OMEX).

Extended functionality

  • CBMPy currently supportes the IBM CPLEX solver (GLPK will again be available soon)
  • Fast parallel FVA is implemented for multicore CPU's     
  • Multiple model editing is supported with support for easily copying modeld components (reaction, species) between models.
  • CBMPy includes methods for model validation and bound integrity checking.
  • CBMPy is used as a core model component for other tools including Metadraft and FAME.  

Installing CBMPy 

CBMPy is available for all major operating systems. The easiest way to install PySCeS is to use a Python package repository like PyPI.

PyPi GitHub Anaconda

 

PyPI (Recommended for CBMPy 0.8.8+)
pip install cbmpy
Update with
pip install -U cbmpy

Conda (older releases)
conda install -c conda-forge -c bgoli cbmpy

Latest source (GitHub see README.md for installation instructions)
git clone https://github.com/SystemsBioinformatics/cbmpy.git

Contact information  

Contact us for questions and to report problems using a GitHub issue.

CBMPy is published on Zenodo please cite the latest release as:
Brett G Olivier, Willi Gottstein, Douwe Molenaar and Bas Teusink. (2023). CBMPy release 0.8.4, Zenodo. https://doi.org/10.5281/zenodo.5546608

Would you like to report an issue, discuss existing or new functionality? Raise an issue on GitHub or contact a developer on Twitter. Older releases are available from the GitHub release page.

This software is developed as part of the modelling activities of the The Systems Biology Lab at the Vrije Universiteit Amsterdam.