BioMet Toolbox: genome-wide analysis of metabolism
Artikel i vetenskaplig tidskrift, 2010

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/.

transcriptional regulation

network

reconstruction

saccharomyces-cerevisiae

fluxes

models

systems biology

Författare

Marija Cvijovic

Kemi- och bioteknik, Livsvetenskaper, Systembiologi

Roberto Olivares Hernandez

Kemi- och bioteknik, Livsvetenskaper, Systembiologi

Rasmus Ågren

Kemi- och bioteknik, Livsvetenskaper, Systembiologi

Niklas Dahr

Chalmers, Kemi- och bioteknik

Wanwipa Vongsangnak

Kemi- och bioteknik, Livsvetenskaper, Systembiologi

Intawat Nookaew

Kemi- och bioteknik, Livsvetenskaper, Systembiologi

K. R. Patil

Danmarks Tekniske Universitet (DTU)

Jens B Nielsen

Kemi- och bioteknik, Livsvetenskaper, Systembiologi

Nucleic Acids Research

0305-1048 (ISSN) 1362-4962 (eISSN)

Vol. 38 W144-W149 gkq404

Styrkeområden

Informations- och kommunikationsteknik

Livsvetenskaper och teknik

Ämneskategorier

Industriell bioteknik

DOI

10.1093/nar/gkq404