Sharing Disease Models

This repository consist of several files implementing very simple disease models to show sharing capabilities of disease models. The models are implemented in PharmML, The MIcroSumlation Tool (MIST), and the SBML tools Tellurium using antimony and Rule Bender using BioNetGen. These examples are supporting the SummerSim 2016 paper titled: "Disease Model Sharing Formats".

FILES:

• README.md - is the file you are reading now
• License.txt - GPL version 3 license file

Representations of Example 1 - Simple Markov Model in paper section 2.2

• categorical_MARKOV1.xml: PharmML format
• Example1.bngl: Rule Bender using BioNetGen implementation
• Example1.py: Tellurium using antimony implementation
• Example1.xml: SBML XML file
• Example1.zip: MIST implementation

Representations of Example 2 - Three State Markov Model in paper section 2.3

• categorical_MARKOV2.xml: PharmML format
• Example2.bngl: Rule Bender using BioNetGen implementation
• Example2.py: Tellurium using antimony implementation
• Example2.xml: SBML XML file
• Example2.zip: MIST implementation

Representations of Example 3 - Stratified Markov Model in paper section 2.4

• categorical_MARKOV3.xml: PharmML format
• Example3.bngl: Rule Bender using BioNetGen implementation
• Example3.py: Tellurium using antimony implementation
• Example3.xml: SBML XML file
• Example3.zip: MIST implementation

USAGE:

Each file uses a different system and format. To run some of the files to reproduce paper results specific tools are required: The following tools and versions were used to generate the results in this paper on a Windows 7 (64 bit) machine:

• MIST Version 0.92.0.0 using Python 2.7.11 | Anaconda 2.4.1 (64-bit) - Install from: https://github.com/Jacob-Barhak/MIST
• RuleBender-2.0.382r3-win32 using BioNetGen-2.2.6 - Install from: http://bionetgen.org/index.php/Download
• Tellurium Version: 1.2.4, RoadRunner version: 1.4.0; Compiler: Microsoft Visual Studio 2013, C++ version: 199711; JIT Compiler: LLVM-3.5; Date: Oct 6 2015, 17:30:09, Antimony version: v2.8.0 - Install from: http://tellurium.analogmachine.org/stuff/

VERSION HISTORY:

Development started after discussion on 22-Sep-2015. Uploaded to Github on 8-March-2016 - no version number assigned

DEVELOPER CONTACT INFO:

Please pass questions according to format to:

SBML

Lucian Smith [email protected]

PharmML

Maciej J. Swat [email protected]

MIST

Jacob Barhak Ph.D. Email: [email protected] http://sites.google.com/site/jacobbarhak/

ACKNOWLEDGEMENTS:

Thanks to discussers in the SBML and DDMoRe discussion lists: Robert Phair, Lukas Endler, Gareth Smith, Nicolas Le Novere, Jose Juan Tapia, Jim Sluka, Leonard Harris, Fengkai Zhang, Nick Holford, Mike K Smith, Sarah Keating, Herbert Sauro, Michael Hucka, Kyle Medley.

LICENSE

Copyright (C) 2015 Jacob Barhak, Maciej J. Swat, Lucian Smith

This file is part of "Sharing Disease Models". "Sharing Disease Models" is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

"Sharing Disease Models" is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

See the GNU General Public License for more details.