SunlightCBM

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SunlightCBM @

SunlightCBM is a suite of perl scripts for constraint-based modelling and flux-balance analysis (FBA) in metabolic networks.

SunlightCBM provides the capability to calculate growth rates and flux distributions for genome-scale reconstructions of metabolic networks given as SBML models, as well as some capabilities for manipulating such models. Features include :

single flux optimisation, flux variability, and systematic reaction deletions,
true −∞ and ∞ for unbounded flux values,
provision of reduced costs and shadow prices,
direct solution of some dual problems,
support for reaction / metabolite addition / removal, and compartment renaming,
compatible with BiGG format SBML models,
extended hierarchical compartment naming,
uses open source LibSBML and GLPK libraries,
designed to work on the command line with unix pipes.

In addition to the online documentation, all the main perl scripts support a --help option, which describes the latest options in detail.

Users interested in FBA may also wish to investigate the openCOBRA toolbox originally from the UCSD Systems Biology group (Bernhard Palsson's lab).

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SunlightCBM 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.

SunlightCBM 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. You should have received a copy of the GNU General Public License along with SunlightCBM. If not, see <http://www.gnu.org/licenses/>.

Copyright is retained by Unilever. Please feel free to get in touch if you want to discuss alternative licensing arrangements

Authors

Patrick Warren (main author), Sílvio M. Duarte Queirós, and Janette Jones.

Contact : patrick.warren{at}unilever.com (sourceforge project admin)