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jmrohwer committed Feb 14, 2024
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2 changes: 1 addition & 1 deletion CITATION.cff
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Expand Up @@ -16,7 +16,7 @@ authors:
title: "The Python Simulator for Cellular Systems: PySCeS"
version: "1.2.0"
repository-code: "https://github.com/PySCeS/pysces/tree/1.2.0"
date-released: 2023-12-14
date-released: 2024-02-14
doi: "10.5281/zenodo.2600905"
license: "BSD-3-Clause"
url: https://pysces.github.io
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -135,4 +135,4 @@ organisations:
* The South African National Bioinformatics Network (2003-2008)
* The South African National Research Foundation (2000-2004)

© Brett G. Olivier & Johann M. Rohwer, April 2023
© Brett G. Olivier & Johann M. Rohwer, February 2024
2 changes: 1 addition & 1 deletion docs
Submodule docs updated 1 files
+2 −2 source/conf.py
2 changes: 1 addition & 1 deletion pysces/PyscesConfig.py
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"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesContrib.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesContribUser.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesInterfaces.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesJWSParse.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesLink.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesMiniModel.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesModel.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesModelMap.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesParScan.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Johann Rohwer ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesParse.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesPlot.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesPlot2.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesSBML.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesSED.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesScan.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesStoich.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesTest.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesUtils.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/PyscesWeb.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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6 changes: 3 additions & 3 deletions pysces/__init__.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Permission to use, modify, and distribute this software is given under the
terms of the PySceS (BSD style) license. See LICENSE.txt that came with
Expand Down Expand Up @@ -40,7 +40,7 @@
this distribution for specifics.
NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OWN RISK.
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
"""

import os
Expand Down Expand Up @@ -513,7 +513,7 @@ def enablePandas(var=True):
)
print('* http://pysces.sourceforge.net *')
## print '* Somewhere In Time *'
print('* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2023 *')
print('* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024 *')
print('* Triple-J Group for Molecular Cell Physiology *')
print('* Stellenbosch University, ZA and VU University Amsterdam, NL *')
print('* PySCeS is distributed under the PySCeS (BSD style) licence, see *')
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2 changes: 1 addition & 1 deletion pysces/_multicorescan.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Johann Rohwer ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/contrib/__init__.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/core2/InfixParser.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
Expand Down
2 changes: 1 addition & 1 deletion pysces/core2/PyscesCore2.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/core2/PyscesCore2Interfaces.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/core2/PyscesCore2Modules.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
Expand Down
2 changes: 1 addition & 1 deletion pysces/core2/__init__.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/kraken/Kraken.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/kraken/KrakenDataTools.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
Expand Down
2 changes: 1 addition & 1 deletion pysces/kraken/KrakenNET.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/kraken/KrakenServer.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
Expand Down
2 changes: 1 addition & 1 deletion pysces/kraken/__init__.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
Expand Down
2 changes: 1 addition & 1 deletion pysces/kraken/controllers/kraken_intersect.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
Expand Down
2 changes: 1 addition & 1 deletion pysces/kraken/startup.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
Expand Down
2 changes: 1 addition & 1 deletion pysces/lib/__init__.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/metatool/__init__.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
Expand Down
2 changes: 1 addition & 1 deletion pysces/nleq2/4.2/__init__.py
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Expand Up @@ -2,7 +2,7 @@
PySCeS - Python Simulator for Cellular Systems
(http://pysces.sourceforge.net)
Copyright (C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr
Stellenbosch, 2004-2023.
Stellenbosch, 2004-2024.
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa
Author: Brett G. Olivier
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2 changes: 1 addition & 1 deletion pysces/nleq2/__init__.py
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@@ -1,7 +1,7 @@
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2023 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Copyright (C) 2004-2024 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier ([email protected])
Triple-J Group for Molecular Cell Physiology
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2 changes: 1 addition & 1 deletion pysces/pitcon/__init__.py
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Expand Up @@ -2,7 +2,7 @@
PySCeS - Python Simulator for Cellular Systems
(http://pysces.sourceforge.net)
Copyright (C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr
Stellenbosch, 2004-2023.
Stellenbosch, 2004-2024.
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa
Author: Brett G. Olivier
Expand Down
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