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]

Reconstruction Models (gene/protein information is not necessary)

Most published metabolic models, assembly of biochemical reactions, are available in either spreedsheet or SBML format.

Available models in Excel: (Please note that the excel files provided here were modified according to Format of database.)

Bacillus subtilis, iYO844 (BiGG), original release, iYO844.xls

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 can be modified by TextReplacer with the replacing rules (RulesforBiGG.TXT) and then imported to GEMSiRV.

Model Name Original Modified Note
E. coli iAF1260 iAF1260.xml Out iAF1260.xml
E. coli textbook textbook.xml Out textbook.xml
H. sapiens Recon 1 Recon1.xml Out Recon1.xml
S. cerevisiae iND750 iND750.xml Out iND750.xml
M. barkeri iAF692 iAF692.xml Out iAF692.xml
H. pylori iIT341 iIT341.xml Out iIT341.xml
S. aureus iSB619 iSB619.xml Out iSB619.xml
M. tuberculosis iNJ661 iNJ661.xml Out iNJ661.xml
E. coli iJO1366 [5] original release Out iJO1366.xml RulesforiJO1366.TXT

Models downloaded from Model SEED can be modified by TextReplacer with the replacing rules (RulesforSEED.TXT) and then imported to GEMSiRV. Because the Model SEED provides more than one hundred of draft models, several of them were listed here as examples.

Model Name Original Modified
Acinetobacter sp. ADP1 ( Opt62977.3 ) Opt62977.3.xml Out Opt62977.3.xml
Bacillus subtilis subsp. subtilis str. 168 ( Seed224308.1 ) Seed224308.1.xml Out Seed224308.1.xml
Staphylococcus aureus subsp. aureus N315 ( Opt158879.1 ) Opt158879.1.xml Out Opt158879.1.xml

In addition to the BiGG- and SEED-based models, several published models were made by using the resource of BioCyc and KEGG. These models can also be modified and imported into the GEMSiRV. For example, the SBML file of Haloalkaliphile Natronomonas pharaonis original release can be modified by TextReplacer with the replacing rules (RulesforKEGG.TXT). The SBML file of EcoCyc (original file metabolic-reactions.sbml) can be modified by the replacing rules (RulesforEcoCyc.TXT) to the modified file (Out metabolic-reactions.xml).

[1] Becker, S. A., A. M. Feist, et al. (2007). "Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox." Nat Protoc 2(3): 727-738.

[2] Palsson, B. (2009). "Metabolic systems biology." FEBS Letters 583(24): 3900-3904.

[3] Feist, A. M., C. S. Henry, et al. (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3: 121.

[4] Liao, Y. C., T. W. Huang, et al. (2011). "An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228." Journal of Bacteriology 193(7): 1710-1717.

[5] Orth, J. D., T. M. Conrad, et al. (2011). "A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011." Mol Syst Biol 7: 535.