PySCeS - Python Simulator for Cellular Systems

PySCeS is a flexible, user-friendly tool for the analysis of cellular systems. For more information please see https://pysces.github.io/

Table of contents

• Introduction
• Installation
• Getting help
• Citing PySCeS
• Contributing
• Licence
• Authors and acknowledgments

Introduction

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

PySCeS releases are available on PyPI, Anaconda.org and Github

PySCeS binaries are available for Python 3.6+ on Windows, Linux and OSX and can be installed using

PyPI

pip install pysces

Anaconda.org

conda install -c conda-forge -c pysces pysces

Building from source

PySCeS requires a Python 3 development environment as well as C++ and FORTRAN compilers to build. For more information please see the INSTALL instructions.

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.

Citing PySCeS

Publication

Brett G. Olivier, Johann M. Rohwer and Jan-Hendrik S. Hofmeyr, Modelling cellular systems with PySCeS, Bioinformatics, Volume 21, Issue 4, 15 February 2005, Pages 560–561, https://doi.org/10.1093/bioinformatics/bti046

Published code releases

PySCeS releases are archived on Zenodo.

Contributing

Primary development is on GitHub, feel free to fork and submit pull requests! Want to add new code to PySCeS, go

Licence

PySCeS is distributed as Open Source software under a BSD style licence, please see LICENCE.txt for details. The licences of software that is bundled with, or used by, PySCeS are available in ADDITIONAL_LICENCES.md.

Authors and acknowledgments

PySCeS main authors are Brett Olivier and Johann Rohwer and in particular, PySCeS founding father Jannie Hofmeyr.

We would also like to acknowledge everyone who has contributed to PySCeS and would like to thank the following (in alphabetical order):

• Evert Bosdriesz
• James Dominy
• Jannie Hofmeyr
• Morgan Hough
• Jonathan Karr
• Ruchir Khandelwal
• Charl Moller
• Danie Palm
• Herbert Sauro
• Lafras Uys

This information can also be found in CONTRIBUTORS.md In addition we would like to acknowledge financial support from the following funding organisations:

• The South African National Bioinformatics Network (2003-2008)
• The South African National Research Foundation (2000-2004)

© Brett G. Olivier & Johann M. Rohwer, August 2021