SunlightCBM
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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)
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