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README.md

PySCeS - Python Simulator for Cellular Systems

The official code repository (http://github.com/PySCeS) of The Python Simulator for Cellular Systems: PySCeS project: http://pysces.sourceforge.net release code will be mirrored on SF SVN and all official source archives and binary releases made available from SourceForge.

PySCeS is available as an Anaconda package for 64 bit Windows, Linux and OSX:

conda install -c sbmlteam -c pysces pysces

Copyright (c) 2004 - 2020, Brett G. Olivier, Johann M. Rohwer and Jan-Hendrik S. Hofmeyr All rights reserved.

PySCeS is distributed under a BSD style licence, please see LICENCE.txt for details

Referring to the latest release

PySCeS is archived on Zenodo DOI:

Brett G Olivier & Johann Rohwer. (2020, March 21). PySCeS/pysces: PySCeS release 0.9.7 (Version 0.9.7). Zenodo. http://doi.org/10.5281/zenodo.2600905

Author information

Brett G. Olivier

Vrije Universiteit Amsterdam Faculty of Earth and Life Sciences Systems Bioinformatics De Boelelaan 1085 NL-1081 HV AMSTERDAM The Netherlands

previous address

Triple-J Group for Molecular Cell Physiology Department of Biochemistry University of Stellenbosch Private Bag X1 Matieland 7602

email: bgoli@users.sourceforge.net web: http://pysces.sourceforge.net

Installation

Please see INSTALL.txt for information on building PySCeS an its modules.

PySCeS is available as an Anaconda package for 64 bit Windows, Linux and OSX:

conda install -c sbmlteam -c pysces pysces

Research software impact

Additional licence information

PySCeS has interfaces to and is distributed with additional packages that are supplied under their own licence conditions.

NLEQ2

The NLEQ2 algorithm from ZIB which has it's own licence and warranty and does not fall under the PySCeS GPL licence. ZIB has kindly given us permission to distribute NLEQ2 with PySCeS provided it's use falls within their terms of usage (/nleq2/nleq2_readme):

You may use or modify this code for your own non commercial purposes for an unlimited time. In any case you should not deliver this code without a special permission of ZIB. In case you intend to use the code commercially, we oblige you to sign an according licence agreement with ZIB.

If you are not using PySCeS for research or personal use you must disable NLEQ2 by setting nleq2 = 0 in setup.py before installation. This is a plug-in solver and its removal does not otherwise influence PySCeS.

Other software (or parts there of) distributed with PySCeS

PLY

David Beazley's PLY 3.3 (http://www.dabeaz.com/ply/). This package is included unchanged and consists of two files lex.py and yacc.py in the lib/ and core2/ modules.

Brett G. Olivier, 21 March 2020

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