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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.

Research software impact

NEW PySCeS is now available as an Anaconda package for 64 bit Windows and Linux:

conda install -c bgoli -c sbmlteam pysces

Copyright (c) 2004 - 2017, 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

Author information

Brett G. Olivier

Vrije Universiteit Amsterdam Faculty of Earth and Life Sciences Department of Molecular Cell Physiology 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.

NEW PySCeS is now available as an Anaconda package for 64 bit Windows and Linux:

conda install -c bgoli -c sbmlteam pysces

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, 22 March 2016