Metabolic Models @Mar 2, 2011 6:14:10 PM

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 the availablitity of GEMsME.

Once the reconstructed models imported into the GEMsME, users can start to add, refine and build their own models and run FBA as well in the GEMsME.

Because two kinds of data formats, spreadsheet and xml, are commonly used for reconstructed metabolic models, the GEMsME 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