SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks

• DOI: 10.1093/bioinformatics/btq679
• Publication Date: 2010-12-11T01:14:58Z
• Authors: Albert Gevorgyan; Michael E. Bushell; Claudio Avignone-...; Andrzej M. Kierzek
• Keywords: Solver; Interface (matter); Metabolic network

Abstract Summary: Constraint-based modeling of genome-scale metabolic networks has been successfully used in numerous applications such as prediction gene essentiality and engineering. We present SurreyFBA, which provides constraint-based simulations network map visualization a free, stand-alone software. In addition to basic simulation protocols, the tool also implements analysis minimal substrate product sets, is useful for engineering nutritional requirements complex vivo environments, but not available other commonly programs. The SurreyFBA based on command line interface GLPK solver distributed binary source code three major operating systems. tool, implemented C++, easily executed within scripting languages bioinformatics community efficient implementation tasks requiring iterative calls linear programming solver. includes JyMet, graphics user allowing spreadsheet-based model presentation, numerical results represented Petri net convention, well charts plots. Availability: under GNU GPL license from http://sysbio3.fhms.surrey.ac.uk/SurreyFBA.zip. Contact: [e-mail]