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

Bioinformatics

Volumn 27, Issue 3, 2011, Pages 433-434

  Gevorgyan, Albert ^a   Bushell, Michael E ^a   Avignone Rossa, Claudio ^a   Kierzek, Andrzej M ^a  

^a UNIVERSITY OF SURREY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; GENOME; HUMAN; METABOLISM; METHODOLOGY;

ANIMALS; COMPUTATIONAL BIOLOGY; GENOME; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; SOFTWARE;

EID: 79551582182     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq679     Document Type: Article

References (10)

1. Alexandrescu,A. et al. (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat. Protoc., 2, 727-738.
2. Beste,D.J.V. et al. (2007) GSMN-TB: a web-based genome scale network model of Mycobacterium tuberculosis metabolism. Genome Biol., 8, r89.
3. Gevorgyan,A. (2009) Theoretical and computational methods for studying genomescale metabolic networks applied to Streptococcus agalactiae. PhD. Thesis, Oxford Brookes University.
4. Gevorgyan,A. et al. (2008) Detection of stoichiometric inconsistencies in biomolecular models. Bioinformatics 24, 2245-2251.
5. Grafahrend-Belau,E. et al. (2009) FBA-SimVis: interactive visualization of constraintbased metabolic models. Bioinformatics, 25, 2755-2757.
6. Heinrich,R. and Schuster,S. (1996) The regulation of cellular systems. Chapman & Hall, London.
7. Khannapho,C. et al. (2008) Selection of objective function in genome scale flux balance analysis for process feed development in antibiotic production. Metab. Eng., 10, 227-233.
8. Lee,D.Y. et al. (2003) MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics, 19, 2144-2146.
9. Price,N.D. et al. (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat. Rev. Microbiol., 2, 886-897.
10. Poolman,M.G. et al. (2006) Challenges to be faced in the reconstruction of metabolic networks from public databases. IEE Proc. Syst. Biol., 153, 379-384.