title: GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization.
abstract: BACKGROUND
  Genome-scale metabolic network models have become an indispensable part of the increasingly important field of systems biology. Metabolic systems biology studies usually include three major components-network model construction, objective- and experiment-guided model editing and visualization, and simulation studies based mainly on flux balance analyses. Bioinformatics tools are required to facilitate these complicated analyses. Although some of the required functions have been served separately by existing tools, a free software resource that simultaneously serves the needs of the three major components is not yet available.
  
  
  RESULTS
  Here we present a software platform, GEMSiRV (GEnome-scale Metabolic model Simulation, Reconstruction and Visualization), to provide functionalities of easy metabolic network drafting and editing, amenable network visualization for experimental data integration and flux balance analysis tools for simulation studies. GEMSiRV comes with downloadable, ready-to-use public-domain metabolic models, reference metabolite/reaction databases and metabolic network maps, all of which can be input into GEMSiRV as the starting materials for network construction or simulation analyses. Furthermore, all of the GEMSiRV-generated metabolic models and analysis results, including projects in progress, can be easily exchanged in the research community. GEMSiRV is a powerful integrative resource that may facilitate the development of systems biology studies.
  
  
  BACKGROUND
  The software is freely available on the web at http://sb.nhri.org.tw/GEMSiRV.
authors.affiliation: Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350, Taiwan, R.O.C.
authors.forename: Yu-Chieh
authors.initials: YC
authors.lastname: Liao
authors.forename: Ming-Hsin
authors.initials: MH
authors.lastname: Tsai
authors.forename: Feng-Chi
authors.initials: FC
authors.lastname: Chen
authors.forename: Chao A
authors.initials: CA
authors.lastname: Hsiung
mesh_terms: D003196:Computer Graphics; D003198:Computer Simulation; D016678:Genome; D023281:Genomics / Q000379:methods*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008954:Models, Biological; D012984:Software; D049490:Systems Biology