GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization

Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface

(2011) Jacek Sroka et al.   BMC BIOINFORMATICS

An Experimentally Validated Genome-Scale Metabolic Reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228

(2011) Y.-C. Liao et al.   JOURNAL OF BACTERIOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format

(2010) T. Forth et al.   BIOINFORMATICS

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

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

(2010) Radhakrishnan Mahadevan et al.   NATURE REVIEWS MICROBIOLOGY

BioMet Toolbox: genome-wide analysis of metabolism

(2010) M. Cvijovic et al.   NUCLEIC ACIDS RESEARCH

FBA-SimVis: interactive visualization of constraint-based metabolic models

(2009) E. Grafahrend-Belau et al.   BIOINFORMATICS

Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001

(2009) Ali Navid et al.   Molecular BioSystems

A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189

(2009) Patrick F. Suthers et al.   PLoS Computational Biology

The Systems Biology Research Tool: evolvable open-source software

(2008) Jeremiah Wright et al.   BMC Systems Biology

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

(2008) Juan Nogales et al.   BMC Systems Biology

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology

(2008) Jacek Puchałka et al.   PLoS Computational Biology