The Python Simulator for Cellular Systems: PySCeS

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-extensible, open source, software actively used and developed by a community of researchers and developers.

Features

• Simulate your time courses with solvers like LSODA and CVODE.
• 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- and concentration-control and response coefficients).
• Auto-generate the stoichiometric matrix and perform structural analysis, determine nullspaces and reduced stoichiometric and MCA matrices.
• Investigate systems which exhibit multiple (stable and unstable) steady-state solutions using a PITCON-based bifurcation analysis module.
• Define models with a 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-dimensional parameter scans.
• Distributed parameter scanning with the ParScanner module within the ipyparallel framework.
• Visualise results of simulations with flexible Matplotlib and Gnuplot interfaces.
• PySCeS supports open community standards for model exchange (SBML) and archiving (SEDML, OMEX).

Installation

PyPI

pip install pysces

Anaconda.org

conda install -c conda-forge -c pysces pysces

Getting help

We currently encourage users to ask questions and request support using a GitHub issue.

General information on PySCeS can be found on the website and extensive documentation on installing, configuring and using PySCeS is available on pyscesdocs.readthedocs.io.