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Where can I find the metabolic network of the human erythrocyte (red blood cell), in SBML format? The red blood cell metabolic network is a model that's usually employed in the literature [see refs below] to demonstrate mathematical techniques of analysis of metabolic networks.

Despite this common use, I haven't been able to find a metabolic network of the human erythrocyte in SBML format, which is commonly employed for these networks (for example, in the BiGG database, http://bigg.ucsd.edu/) because it is easy to use with the COBRA package (http://opencobra.sourceforge.net/).

So, anyone can tell me where I can find an SBML model of the metabolic network of the human red blood cell?

References where the red blood cell metabolic network is used:

  • Wiback, S. J., Famili, I., Greenberg, H. J., & Palsson, B. Ø. (2004). Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space. Journal of Theoretical Biology, 228, 437–447. doi:10.1016/j.jtbi.2004.02.006

  • Braunstein, A., Mulet, R., & Pagnani, A. (2008). Estimating the size of the solution space of metabolic networks. BMC Bioinformatics, 9, 240. doi:10.1186/1471-2105-9-240

  • Jamshidi, N., Edwards, J. S., Fahland, T., Church, G. M., & Palsson, B. Ø. (2001). Dynamic simulation of the human red blood cell metabolic network. Bioinformatics, 17(3), 286–287.

  • Kauffman, K. J., Pajerowski, J. D., Jamshidi, N., Palsson, B. Ø., & Edwards, J. S. (2002). Description and analysis of metabolic connectivity and dynamics in the human red blood cell. Biophysical Journal, 83(2), 646–662. doi:10.1016/S0006-3495(02)75198-9

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1 Answer 1

The model used by Jamshidi et al. can be found in the BioModels database with acession no. MODEL1103210001 http://www.ebi.ac.uk/compneur-srv/biomodels-main/MODEL1103210001

A more recent model has also been described in Bordbar et al. iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. BMC Systems Biology 2011, 5:110 The model file in SBML format can be downloaded from the Additional Files section (http://www.biomedcentral.com/1752-0509/5/110/additional) or BioModels (http://www.ebi.ac.uk/compneur-srv/biomodels-main/MODEL1106080000).

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What about the model used by Wiback et al? The paper has the stechiometric matrix, but in pdf format, which is useless. –  becko Feb 18 at 13:15
    
Indeed, I couldn't find any model file for that. I wouldn't call it completely useless though. If you are using for example COBRA Toolbox or CobraPy, you can construct the model yourself from the matrix, then save it to SBML. I'd expect to use a couple of hours. –  jarlemag Feb 22 at 9:41

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