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bioRxiv · 10.1101/245068

A Portable Structural Analysis Library for Reaction Networks

Bedaso, Y. M.·Bergmann, F.·Choi, K. M.·Sauro, H. M.
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Abstract

The topology of a reaction network can have a significant influence on the networks dynamical properties. Such influences can include constraints on network flows and concentration changes or more insidiously result in the emergence of feedback loops. These effects are due entirely to mass constraints imposed by the network configuration and are important considerations before any dynamical analysis is made. Most established simulation software tools usually carry out some kind of structural analysis of a network before any attempt is made at dynamic simulation. In this paper we describe a portable software library, libStructural, that can carry out a variety of popular structural analyses that includes conservation analysis, flux dependency analysis and enumerating elementary modes. The library employs robust algorithms that allow it to be used on large networks with more than a two thousand nodes. The library accepts either a raw or fully labeled stoichiometry matrix or models written in SBML format. The software is written in standard C/C++ and comes with documentation and a test suite. The software is available for Windows, Mac OS X, and can be compiled easily on any Linux operating system. A language binding for Python is also available through the pip package manager making it trivial to install on any standard Python distribution. As a second example, we also create a new libStructural plugin for PathwayDesigner that allows solutions to be viewed graphically. The source code is licensed under the open source BSD license and is available on GitHub (https://github.com/sys-bio/Libstructural)

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Bedaso, Y. M., Bergmann, F., Choi, K. M., Sauro, H. M.. 2018-01-08. A Portable Structural Analysis Library for Reaction Networks. https://doi.org/10.1101/245068

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