Metabolic Models

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 GEMSiRV.

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

Because two kinds of data formats, spreadsheet and xml, are commonly used for reconstructed metabolic models, the GEMSiRV allows importing both formats.

Reconstruction Models (GPR)

Two-layer relations: "gene and protein" and "protein and reaction" can be described in a three-sheet spreadsheet including Gene Index, Protein Index and Reaction Index.

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: ec-core.xls (modified from ecoli_core_model.xls), iAF1260 GPR.xls[3], iYL1228 GPR.xls[4]