Genome-scale metabolic network reconstruction is important for understanding cellular behaviors in a systems view.
Converting the reconstruction into a mathematical model enables researchers to analyze cell behaviors in response to changing environments by using constraint-based flux balance analysis (FBA) tools, such as COBRA [1].
With the growing availability of complete microbial genomes, the number of genome-scale metabolic networks is expected to increase rapidly.
However, the number of genome-scale metabolic models follows in single-digit percentage of the number of sequenced genomes due to the difficulties in network reconstruction [2].
Availabe genome-scale metabolic network reconstructions were collected and listed in Palsson's Systems Biology Research Group.
Here, we took the adavantage of these reconstructed metabolic networks to demonstrate how the Model Editor works.
Because two kinds of data formats, spreadsheet and xml, are commonly used for metabolic reconstruction models, the Model Editor allows importing both formats.
Reconstruction Models (GPR)
Two layers of relations between "gene and protein" and "protein and reaction" can be summarized in a three-sheet spreadsheet.
Gene Index (A basic description of gene)
5'Coordinate, Locus Tag, Gene, Product, EC Number
Protein Index (Protein information and the association between protein and gene)
Abbreviation, Name, Gene
Reaction Index (Reaction information and the association between reaction and protein)
Abbreviation, Name, Equation, Protein, Subsystem
Available models: iAF1260 GPR.xls, iYL1228
Reconstruction Models Most published metabolic models, assembly of biochemical reactions, are available in either spreedsheet or SBML format. Available models in Excel:
Bacillus subtilis, iYO844 (BiGG), original release, iYO844.xls [3] Buchnera aphidicola, iGT196 (BiGG), original release, iGT196.xls Saccharomyces cerevisiae, iMM904 (BiGG), original release, iMM904.xls Salmonella typhimurium,iRR1083 (BiGG), original release, iRR1083.xls Shewanella oneidensis, iSO783 (BiGG), original Release, iSO783.xls Available models in SBML:
Models exported from BiGG, e.g. E. coli iAF1260, Downloaded from Model SEED, e.g. [1] Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ: Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2007, 2(3):727-738. [2] Palsson B: Metabolic systems biology. FEBS Lett 2009, 583(24):3900-3904. [3] Please note that the excel files provided here were modified according to Reference Databases.