MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks

CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED

(2012) Matthew DeJongh et al.   BIOINFORMATICS

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

(2012) Akhil Kumar et al.   BMC BIOINFORMATICS

FAME, the Flux Analysis and Modeling Environment

(2012) Joost Boele et al.   BMC Systems Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

OptFlux: an open-source software platform for in silico metabolic engineering

(2010) Isabel Rocha et al.   BMC Systems Biology

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

The application of flux balance analysis in systems biology

(2009) Erwin P. Gianchandani et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Genome-scale metabolic networks

(2009) Marco Terzer et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY