title: BioMet Toolbox: genome-wide analysis of metabolism.
abstract: The rapid progress of molecular biology tools for directed genetic modifications, accurate quantitative experimental approaches, high-throughput measurements, together with development of genome sequencing has made the foundation for a new area of metabolic engineering that is driven by metabolic models. Systematic analysis of biological processes by means of modelling and simulations has made the identification of metabolic networks and prediction of metabolic capabilities under different conditions possible. For facilitating such systemic analysis, we have developed the BioMet Toolbox, a web-based resource for stoichiometric analysis and for integration of transcriptome and interactome data, thereby exploiting the capabilities of genome-scale metabolic models. The BioMet Toolbox provides an effective user-friendly way to perform linear programming simulations towards maximized or minimized growth rates, substrate uptake rates and metabolic production rates by detecting relevant fluxes, simulate single and double gene deletions or detect metabolites around which major transcriptional changes are concentrated. These tools can be used for high-throughput in silico screening and allows fully standardized simulations. Model files for various model organisms (fungi and bacteria) are included. Overall, the BioMet Toolbox serves as a valuable resource for exploring the capabilities of these metabolic networks. BioMet Toolbox is freely available at www.sysbio.se/BioMet/.
authors.affiliation: Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.
authors.forename: Marija
authors.initials: M
authors.lastname: Cvijovic
authors.forename: Roberto
authors.initials: R
authors.lastname: Olivares-Hernández
authors.forename: Rasmus
authors.initials: R
authors.lastname: Agren
authors.forename: Niklas
authors.initials: N
authors.lastname: Dahr
authors.forename: Wanwipa
authors.initials: W
authors.lastname: Vongsangnak
authors.forename: Intawat
authors.initials: I
authors.lastname: Nookaew
authors.forename: Kiran Raosaheb
authors.initials: KR
authors.lastname: Patil
authors.forename: Jens
authors.initials: J
authors.lastname: Nielsen
mesh_terms: D000465:Algorithms; D000431:Ethanol / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D016678:Genome; D005947:Glucose / Q000378:metabolism; D020407:Internet; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D025941:Protein Interaction Mapping; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors; D000431:Ethanol; D005947:Glucose