PySCeS

 

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

Computer modelling has become an integral tool in the analysis and understanding of the reaction networks that underlie cellular processes. PySCeS, first released in 2003, is extremely flexible, user-extendible, open source, software actively used and developed by a community of researchers and developers.

The latest PySCeS release is version 1.2.2 (August 2024).

 

User friendly

  • Define models with human readable, Model Description Language.
  • Use the full power of Python available to test, build and share your modelling experiments.
  • User friendly methods for generating and 1, 2 and n-dimension parameter scans.
  • Visualise results of simulations with flexible Matplotlib and Gnuplot interfaces.
  • PySCeS supports open community standards for model exchange (SBML) and archiving (SEDML, OMEX).

Modelling features

  • Simulate your time courses with solvers like LSODA.
  • Efficiently determine steady states using a selection of non-linear, root-finding algorithms (e.g. HYBRD, NLEQ2).
  • Use Metabolic Control Analysis (MCA) to investigate control and regulation of cellular systems (elasticities, flux control and response coefficients).
  • Perform structural analysis and determine nullspaces and reduced stoichiometric and MCA matrices
  • Investigate systems which exhibit multiple (stable and unstable) steady-state solutions using PITCON based bifurcation analysis module.

Installing PySCeS 

PySCeS is available for all major operating systems. The easiest way to install PySCeS is to use a Python package manager.

PyPi GitHub Anaconda
  • PyPI
    pip install pysces
  • Conda
    conda install -c conda-forge -c pysces pysces
  • Latest source (GitHub see install.md for instructions)
    git clone https://github.com/PySCeS/pysces.git

The main branch contains the latest release code, for the latest development code, checkout the development branch. I you would like to contribute to PySCeS please do so using pull requests against development.

Contact us  

  • Chat to a developer or user community? Try the PySCeS Google group.
  • Report a specific code issue or discuss existing or new functionality? Create an issue on the PySCeS GitHub repository.

Live demo 

Click the button below to try PySCeS in a JupyterLab environment; an example notebook and models are provided. Note that this runs in a web-assembly environment and any changes are saved to your local browser storage, which is not persistent. When the browser cache or site data are cleared, any modifications will be lost.

Try PySCeS

Documentation

For more information on using and citing PySCeS try the documentation or 2005 Bioinformatics publication.

Documentation Publication

 

PySCeS source code, issue tracker and wiki available on GitHub and see who is citing PySCeS on Google Scholar.

PySCeS releases are archived on Zenodo and can be referred to as DOI: 10.5281/zenodo.2600905