This is a collection of published GEMs that have been converted to the YAML format used by PSAMM, using the psamm-import tool. These model files serve as an easy way for people interested in PSAMM to get started on working with these models.
The models in this repository were originally used for the analysis performed in the following publication but the files here have been updated since the publication to follow more recent conventions of the PSAMM software. To access the model files as they were originally used, please use the archived-models branch.
Steffensen JL, Dufault-Thompson K, Zhang Y. PSAMM: A Portable System for the
Analysis of Metabolic Models. PLOS Comput Biol. Public Library of Science;
2016;12: e1004732. 10.1371/journal.pcbi.1004732.
The original files for the models were obtained from the publications referenced in the tables below (unless otherwise noted). During the analysis of the models, some models had issues corrected which are summarized in the first table below. The table also references the Git commits that document the exact changes that were made to the model files.
No files in this repository are original model publications. To obtain the original model files please consult the original publications listed below.
The collection of models is split into three sections:
- sbml: Models that have been loaded as SBML files using the sbml loader in psamm-import.
- excel: Models that have been loaded using a model-specific Excel file loader in psamm-import.
- matlab: Models that have been loaded from MATLAB data files using the PSAMM MATLAB importer.
| Model | Correction(s) | Commit(s) |
|---|---|---|
| iJN746 | Corrected compound references to cardiolipins in biomass reaction to refer to cardiolipins in the periplasm. | 7d68a62 |
| iKF1028 | Corrected stoichiometric balances. | 8791efa |
| iMA871 | 1. Added missing exchange reaction for BIOMASS compound and removed duplicate compounds in a number of reactions. 2. Added biomass reaction definition. | 1. b10e858, 2. b4249ed |
| iRsp1095 | 1. Changed medium for growth based on medium description in [Imam et al. 2011] (https://doi.org/10.1186/1752-0509-5-116). 2. Made all lower exchange bounds zero. 3. Marked zeromass compounds. 4. Added biomass reaction definition. | 1. 3340d7a, 2. 15f48dc, 3. 405ee9d, 4. b4249ed |
| iSyn731 | Updated to new model from http://www.maranasgroup.com/models.htm downloaded on September 9, 2015. | ca39f98 |
| RECON1 | Fixed stoichiometric consistency. | f72da25 |
| RECON2 | Fixed stoichiometric consistency. | 5671060 |
| AORYZAE_COBRA | 1. Allowed essential compounds in medium. 2. Added biomass reaction definition. | 1. 134968f, 2. b4249ed |
| iCce806 | 1. Marked zeromass compounds. 2. Added biomass reaction definition. | 1. 405ee9d, 2. b4249ed |
| iRC1080 | 1. Marked zeromass compounds. 2. Added biomass reaction definition. | 1. 405ee9d, 2. b4249ed |
| iFF708 | Allowed essential compounds in medium. | f6a6f76 |
| Multiple Models | Marked zeromass compounds in the following four models: iJN678, iRS1563, iRS1597, and iSyn669. | 405ee9d |
| Multiple Models | Added biomass reaction definitions in the following seventeen models: AbyMBEL891, PpaMBEL1254, PpuMBEL1071, S_coelicolor, SpoMBEL1693, VvuMBEL943, iAC560, iAI549, iLC915, iMA945, iMM1415, iMO1056, iMR1_799, iPS189, iSR432, iSS884, and mus_musculus. | b4249ed |
| Model | Reference |
|---|---|
| AORYZAE_COBRA | Vongsangnak W, Olsen P, Hansen K, Krogsgaard S, Nielsen J (2008) Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae. BMC Genomics 9: 245. https://doi.org/10.1186/1471-2164-9-245. |
| AbyMBEL891 | Kim HU, Kim TY, Lee SY (2010) Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE. Mol Biosyst 6: 339–348. https://doi.org/10.1039/b916446d. |
| AlgaGEM | Gomes de Oliveira Dal’Molin, C., Quek, L.-E., Palfreyman, R. W., & Nielsen, L. K. (2011). AlgaGEM – a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome. BMC Genomics, 12(Suppl 4), S5. https://doi.org/10.1186/1471-2164-12-s4-s5 |
| AraGEM | de Oliveira Dal’Molin C. G., Quek L. E., Palfreyman R. W., Brumbley S. M. & Nielsen L. K. AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis. Plant Physiol. 152(2), 579–589 (2010). |
| NmrFL413 | Li, F., Xie, W., Yuan, Q., Luo, H., Li, P., Chen, T., Ma, H. (2018). Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea. AMB Express, 8(1). https://doi.org/10.1186/s13568-018-0635-y |
| PpaMBEL1254 | Sohn, Seung Bum, Alexandra B. Graf, Tae Yong Kim, Brigitte Gasser, Michael Maurer, Pau Ferrer, Diethard Mattanovich, and Sang Yup Lee. Genome-scale Metabolic Model of Methylotrophic Yeast Pichia Pastoris and Its Use for in Silico Analysis of Heterologous Protein Production. Biotechnology Journal, 2010, 705-15. |
| PpuMBEL1071 | Sohn, Seung Bum, Tae Yong Kim, Jong Myoung Park, and Sang Yup Lee. In Silico Genome-scale Metabolic Analysis of Pseudomonas Putida KT2440 for Polyhydroxyalkanoate Synthesis, Degradation of Aromatics and Anaerobic Survival. Biotechnology Journal, 2010, 739-50. |
| RECON1 | Duarte, N. C., S. A. Becker, N. Jamshidi, I. Thiele, M. L. Mo, T. D. Vo, R. Srivas, and B. O. Palsson. Global Reconstruction of the Human Metabolic Network Based on Genomic and Bibliomic Data. Proceedings of the National Academy of Sciences, 2007, 1777-782. |
| RECON2 | Thiele, Ines, Neil Swainston, Ronan M T Fleming, Andreas Hoppe, Swagatika Sahoo, Maike K. Aurich, Hulda Haraldsdottir, Monica L. Mo, Ottar Rolfsson, Miranda D. Stobbe, Stefan G. Thorleifsson, Rasmus Agren, Christian Bölling, Sergio Bordel, Arvind K. Chavali, Paul Dobson, Warwick B. Dunn, Lukas Endler, David Hala, Michael Hucka, Duncan Hull, Daniel Jameson, Neema Jamshidi, Jon J. Jonsson, Nick Juty, Sarah Keating, Intawat Nookaew, Nicolas Le Novère, Naglis Malys, Alexander Mazein, Jason A. Papin, Nathan D. Price, Evgeni Selkov, Martin I. Sigurdsson, Evangelos Simeonidis, Nikolaus Sonnenschein, Kieran Smallbone, Anatoly Sorokin, Johannes H G M Van Beek, Dieter Weichart, Igor Goryanin, Jens Nielsen, Hans V. Westerhoff, Douglas B. Kell, Pedro Mendes, and Bernhard Ø Palsson. A Community-driven Global Reconstruction of Human Metabolism. Nat Biotechnol Nature Biotechnology 31.5 (2013): 419-25. |
| Recon3D | King, Z. A., Lu, J., Dräger, A., Miller, P., Federowicz, S., Lerman, J. A., Ebrahim, A., Palsson, B. O., & Lewis, N. E. (2015). BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Research, 44(D1), D515–D522. https://doi.org/10.1093/nar/gkv1049 |
| STM_v1.0 | Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, et al. (2011) A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst Biol 5: 8. https://doi.org/10.1186/1752-0509-5-8. |
| S_coelicolor | Alam, Mohammad T., et al. "Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor." BMC genomics 11.1 (2010): 202. https://doi.org/10.1186/1471-2164-11-202. |
| S_coelicolor_fixed | Alam, Mohammad T., et al. "Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor." BMC genomics 11.1 (2010): 202. https://doi.org/10.1186/1471-2164-11-202. Fixed model from m_model_collection. |
| SpoMBEL1693 | Sohn SB, Kim TY, Lee JH, Lee SY (2012) Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth. https://doi.org/10.1186/1752-0509-6-49. |
| VvuMBEL943 | Kim, H. U., S. Y. Kim, H. Jeong, T. Y. Kim, J. J. Kim, H. E. Choy, K. Y. Yi, J. H. Rhee, and S. Y. Lee. Integrative Genome-scale Metabolic Analysis of Vibrio Vulnificus for Drug Targeting and Discovery. Molecular Systems Biology 7.1 (2011): 460. Web. |
| iAC560 | Chavali, Arvind K., Jeffrey D. Whittemore, James A. Eddy, Kyle T. Williams, and Jason A. Papin. Systems Analysis of Metabolism in the Pathogenic Trypanosomatid Leishmania Major. Mol Syst Biol Molecular Systems Biology 4 (2008): n. pag. Web. |
| iAF1260 | Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, 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. https://doi.org/10.1038/msb4100155. |
| iAF692 | Feist, Adam M., Johannes C M Scholten, Bernhard Ø Palsson, Fred J. Brockman, and Trey Ideker. Modeling Methanogenesis with a Genome-scale Metabolic Reconstruction of Methanosarcina Barkeri. Mol Syst Biol Molecular Systems Biology 2 (2006): n. pag. |
| iAI549 | Ahsanul Islam M, Edwards EA, Mahadevan R (2010) Characterizing the metabolism of Dehalococcoides with a constraint-based model. PLoS Comput Biol 6. https://doi.org/10.1371/journal.pcbi.1000887. |
| iBsu1103 | Henry CS, Zinner JF, Cohoon MP, Stevens RL. iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biol. 2009;10(6):R69. https://doi.org/10.1186/gb-2009-10-6-r69. |
| iAK888 | Klanchui, A., Dulsawat, S., Chaloemngam, K., Cheevadhanarak, S., Prommeenate, P., & Meechai, A. (2018). An Improved Genome-Scale Metabolic Model of Arthrospira platensis C1 (iAK888) and Its Application in Glycogen Overproduction. Metabolites, 8(4), 84. https://doi.org/10.3390/metabo8040084 |
| iAp386B454 | Pelicaen, R., Gonze, D., Teusink, B., De Vuyst, L., & Weckx, S. (2019). Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation. Frontiers in Microbiology, 10. https://doi.org/10.3389/fmicb.2019.02801 |
| iCA1273 | Archer CT, Kim JF, Jeong H, Park JH, Vickers CE, et al. (2011) The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli. BMC Genomics 12: 9. https://doi.org/10.1186/1471-2164-12-9. |
| iCB925 | Milne, Caroline B., et al. Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. BMC systems biology 5.1 (2011): 130. https://doi.org/10.1186/1752-0509-5-130. |
| iCac802 | Dash, S., Mueller, T. J., Venkataramanan, K. P., Papoutsakis, E. T., & Maranas, C. D. (2014). Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model. Biotechnology for Biofuels, 7(1), 144. |
| iCce806 | Vu TT, Stolyar SM, Pinchuk GE, Hill EA, Kucek LA, et al. (2012) Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142. PLoS Comput Biol 8(4): e1002460. https://doi.org/10.1371/journal.pcbi.1002460. |
| iCHOv1_final | Hefzi, H., Ang, K. S., Hanscho, M., Bordbar, A., Ruckerbauer, D., Lakshmanan, M., Orellana, C. A., Baycin-Hizal, D., Huang, Y., Ley, D., Martinez, V. S., Kyriakopoulos, S., Jiménez, N. E., Zielinski, D. C., Quek, L.-E., Wulff, T., Arnsdorf, J., Li, S., Lee, J. S., … Lewis, N. E. (2016). A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Systems, 3(5), 434–443.e8. https://doi.org/10.1016/j.cels.2016.10.020 |
| iCZ946 | Zuñiga, C., Levering, J., Antoniewicz, M. R., Guarnieri, M. T., Betenbaugh, M. J., & Zengler, K. (2017). Predicting Dynamic Metabolic Demands in the Photosynthetic Eukaryote Chlorella vulgaris. Plant Physiology, 176(1), 450–462. https://doi.org/10.1104/pp.17.00605 |
| iFF708 | Forster, J. Genome-Scale Reconstruction of the Saccharomyces Cerevisiae Metabolic Network. Genome Research 13.2 (2003): 244-53. Web. |
| iCZ843 | Zuñiga, C., Li, C.-T., Huelsman, T., Levering, J., Zielinski, D. C., McConnell, B. O., Long, C. P., Knoshaug, E. P., Guarnieri, M. T., Antoniewicz, M. R., Betenbaugh, M. J., & Zengler, K. (2016). Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions. Plant Physiology, 172(1), 589–602. https://doi.org/10.1104/pp.16.00593 |
| iIB711 | Borodina, Irina, Preben Krabben, and Jens Nielsen. Genome-scale analysis of Streptomyces coelicolor A3 (2) metabolism. Genome research 15.6 (2005): 820-829. https://doi.org/10.1101/gr.3364705. |
| iIT341 | Thiele, Ines, et al. Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single-and double-deletion mutants. Journal of bacteriology 187.16 (2005): 5818-5830. https://doi.org/10.1128/JB.187.16.5818-5830.2005. |
| iJN678 | Nogales J, Gudmundsson S, Knight EM, Palsson BO, Thiele I (2012) Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis. Proc Natl Acad Sci U S A 109: 2678–2683. https://doi.org/10.1073/pnas.1117907109. |
| iJN746 | Nogales J, Palsson BØ, Thiele I (2008) A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol 2: 79. https://doi.org/10.1186/1752-0509-2-79. |
| iJO1366 | Orth JD, Conrad TM, Na J, Lerman JA, Nam H, et al. (2011) A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011. Mol Syst Biol 7. https://doi.org/10.1038/msb.2011.65. |
| iJP815 | Puchalka, J., M.A. Oberhardt, M. Godinho, A. Bielecka, D. Regenhardt, K.N. Timmis, J.A. Papin, and V.A.P. Martins dos Santos. 2008. Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Computational Biology, 4(10):e1000210 |
| iJR904 | Reed JL, Vo TD, Schilling CH, Palsson BO. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome biology. 2003. January;4(9):R54 |
| iRJ1321 | Shah, A. R., Ahmad, A., Srivastava, S., & Jaffar Ali, B. M. (2017). Reconstruction and analysis of a genome-scale metabolic model of Nannochloropsis gaditana. Algal Research, 26, 354–364. https://doi.org/10.1016/j.algal.2017.08.014 |
| iKF1028 | Fang K, Zhao H, Sun C, Lam CMC, Chang S, et al. (2011) Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction. BMC Syst Biol 5: 83. https://doi.org/10.1186/1752-0509-5-83. |
| iLB1027_lipid | Levering, J., Broddrick, J., Dupont, C. L., Peers, G., Beeri, K., Mayers, J., Gallina, A. A., Allen, A. E., Palsson, B. O., & Zengler, K. (2016). Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. PLOS ONE, 11(5), e0155038. https://doi.org/10.1371/journal.pone.0155038 |
| iLC915 | Caspeta, Luis, et al. Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. BMC systems biology 6.1 (2012): 24. https://doi.org/10.1186/1752-0509-6-24. |
| iMA871 | Andersen, Mikael Rørdam, Michael Lynge Nielsen, and Jens Nielsen. Metabolic Model Integration of the Bibliome, Genome, Metabolome and Reactome of Aspergillus Niger. Mol Syst Biol Molecular Systems Biology, 2008. |
| iMA945 | AbuOun M, Suthers PF, Jones GI, Carter BR, Saunders MP, et al. (2009) Genome scale reconstruction of a salmonella metabolic model comparison of similarity and differences with a commensal Escherichia coli strain. J Biol Chem 284: 29480–29488. https://doi.org/10.1074/jbc.M109.005868. |
| iMB745 | Benedict, M. N., M. C. Gonnerman, W. W. Metcalf, and N. D. Price. Genome-Scale Metabolic Reconstruction and Hypothesis Testing in the Methanogenic Archaeon Methanosarcina Acetivorans C2A. Journal of Bacteriology, 2011, 855-65. |
| iMG746 | Gonnerman, M. C., Benedict, M. N., Feist, A. M., Metcalf, W. W., & Price, N. D. (2013). Genomically and biochemically accurate metabolic reconstruction ofMethanosarcina barkeriFusaro, iMG746. Biotechnology Journal, 8(9), 1070–1079. https://doi.org/10.1002/biot.201200266 |
| iMM1415 | Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BØ (2010) A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. BMC Syst Biol 4: 140. https://doi.org/10.1186/1752-0509-4-140. |
| iMM904 | Mo ML, Palsson BO, Herrgård MJ (2009) Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst Biol 3: 37. https://doi.org/10.1186/1752-0509-3-37. |
| iMO1056 | Oberhardt, M.A., J. Puchalka, K.E. Fryer, V.A.P. Martins dos Santos, and J.A. Papin. 2008. Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. Journal of Bacteriology, 190(8). |
| iMR1_799 | Ong WK, Vu TT, Lovendahl KN, Llull JM, Serres MH, et al. (2014) Comparisons of Shewanella strains based on genome annotations, modeling, and experiments. BMC Syst Biol 8: 1–11. |
| iND750 | Duarte NC, Herrgård MJ, Palsson BØ (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14: 1298–1309. https://doi.org/10.1101/gr.2250904. |
| iMZ1055 | Zou, W., Zhou, M., Liu, L., & Chen, J. (2013). Reconstruction and analysis of the industrial strain Bacillus megaterium WSH002 genome-scale in silico metabolic model. Journal of Biotechnology, 164(4), 503–509. https://doi.org/10.1016/j.jbiotec.2013.01.019 |
| iNJ661 | Jamshidi, Neema, and Bernhard Ø. Palsson. "Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets." BMC systems biology 1.1 (2007): 26. https://doi.org/10.1186/1752-0509-1-26. |
| iNJ661v | Fang X, Wallqvist A, Reifman J: Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis. BMC Syst Biol 2010, 4:160. |
| iNJ661m | Fang X, Wallqvist A, Reifman J: Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis. BMC Syst Biol 2010, 4:160. |
| iNS934 | Loira, N., Mendoza, S., Paz Cortés, M., Rojas, N., Travisany, D., Genova, A. D., Gajardo, N., Ehrenfeld, N., & Maass, A. (2017). Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production. BMC Systems Biology, 11(1). https://doi.org/10.1186/s12918-017-0441-1 |
| iOD907 | Dias, O., Pereira, R., Gombert, A. K., Ferreira, E. C., & Rocha, I. (2014). iOD907, the first genome-scale metabolic model for the milk yeastKluyveromyces lactis. Biotechnology Journal, 9(6), 776–790. https://doi.org/10.1002/biot.201300242 |
| iPS189 | Suthers, Patrick F., Madhukar S. Dasika, Vinay Satish Kumar, Gennady Denisov, John I. Glass, and Costas D. Maranas. A Genome-Scale Metabolic Reconstruction of Mycoplasma Genitalium, IPS189. PLoS Comput Biol PLoS Computational Biology, 2009. |
| iPS189_fixed | Suthers, Patrick F., Madhukar S. Dasika, Vinay Satish Kumar, Gennady Denisov, John I. Glass, and Costas D. Maranas. A Genome-Scale Metabolic Reconstruction of Mycoplasma Genitalium, IPS189. PLoS Comput Biol PLoS Computational Biology, 2009. Fixed model from m_model_collection. |
| iRC1080 | Chang RL, Ghamsari L, Manichaikul A, Hom EFY, Balaji S, et al. (2011) Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol Syst Biol 7: 518. https://doi.org/10.1038/msb.2011.52. |
| iRS1563 | Saha R, Suthers PF, Maranas CD (2011) Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism. PLoS ONE 6(7): e21784. https://doi.org/10.1371/journal.pone.0021784. |
| iRS1597 | Saha R, Suthers PF, Maranas CD (2011) Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism. PLoS ONE 6(7): e21784. https://doi.org/10.1371/journal.pone.0021784. |
| iRsp1095 | Imam, Saheed, et al. iRsp1095: a genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network. BMC systems biology 5.1 (2011): 116. https://doi.org/10.1186/1752-0509-5-116. |
| iSB619 | Becker, S.A. and Pallson B.O. Genome-scale reconstruction of the metabolic network in Staphylococcus auresus N315: an initial draft to the two-dimensional annotation. BMC Microbiol., 5, 8, 2005. |
| iSR432 | Roberts SB, Gowen CM, Brooks JP, Fong SS (2010) Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production. BMC Syst Biol 4: 31. https://doi.org/10.1186/1752-0509-4-31. |
| iSS884 | Caspeta, Luis, et al. Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. BMC systems biology 6.1 (2012): 24. https://doi.org/10.1186/1752-0509-6-24. |
| iSyn669 | Montagud, Arnau, Emilio Navarro, Pedro Fernández De Córdoba, Javier F. Urchueguía, and Kiran Patil. Reconstruction and Analysis of Genome-scale Metabolic Model of a Photosynthetic Bacterium. BMC Systems Biology BMC Syst Biol 4.1 (2010): 156. |
| iSyn731 | Saha R, Verseput AT, Berla BM, Mueller TJ, Pakrasi HB, et al. (2012) Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. PLoS One 7. https://doi.org/10.1371/journal.pone.0048285. |
| iTH366 | Plata G, Hsiao T-L, Olszewski KL, Llinás M, Vitkup D (2010) Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. Mol Syst Biol 6: 408. https://doi.org/10.1038/msb.2010.60. |
| iTZ479 | Zhang, Y., I. Thiele, D. Weekes, Z. Li, L. Jaroszewski, K. Ginalski, A. M. Deacon, J. Wooley, S. A. Lesley, I. A. Wilson, B. Palsson, A. Osterman, and A. Godzik. Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga Maritima. Science 325.5947 (2009): 1544-549 |
| iVS941 | Kumar, Vinay Satish, James G. Ferry, and Costas D. Maranas. Metabolic Reconstruction of the Archaeon Methanogen Methanosarcina Acetivorans. BMC Systems Biology BMC Syst Biol 5.1 (2011): 28 |
| iVS941_fixed | Kumar, Vinay Satish, James G. Ferry, and Costas D. Maranas. Metabolic Reconstruction of the Archaeon Methanogen Methanosarcina Acetivorans. BMC Systems Biology BMC Syst Biol 5.1 (2011): 28. Fixed model from m_model_collection. |
| iWZ583 | Zou, W., Xiong, X., Zhang, J., Zhang, K., Zhao, X., & Zhao, C. (2018). Reconstruction and analysis of a genome-scale metabolic model of Methylovorus sp. MP688, a high-level pyrroloquinolone quinone producer. Biosystems, 172, 37–42. https://doi.org/10.1016/j.biosystems.2018.07.009 |
| iYL1228 | Liao, Yu-Chieh, et al. An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. Journal of bacteriology 193.7 (2011): 1710-1717. https://doi.org/10.1128/JB.01218-10. |
| mus_musculus | Lake-ee Quek and Lars K. Nielsen (2008) On the Reconstruction of the Mus musculus Genome-scale Metabolic Network Model. Genome Informatics 2008: pp. 89-100. https://doi.org/10.1142/9781848163324_0008. |
| Model | Reference |
|---|---|
| STM_v1.0 | Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, et al. (2011) A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst Biol 5: 8. https://doi.org/10.1186/1752-0509-5-8. |
| iCce806 | Vu TT, Stolyar SM, Pinchuk GE, Hill EA, Kucek LA, et al. (2012) Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142. PLoS Comput Biol 8(4): e1002460. https://doi.org/10.1371/journal.pcbi.1002460. |
| iJO1366 | Orth JD, Conrad TM, Na J, Lerman JA, Nam H, et al. (2011) A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011. Mol Syst Biol 7. https://doi.org/10.1038/msb.2011.65. |
| iMA945 | AbuOun M, Suthers PF, Jones GI, Carter BR, Saunders MP, et al. (2009) Genome scale reconstruction of a salmonella metabolic model comparison of similarity and differences with a commensal Escherichia coli strain. J Biol Chem 284: 29480–29488. https://doi.org/10.1074/jbc.M109.005868. |
| iMR1_799 | Ong WK, Vu TT, Lovendahl KN, Llull JM, Serres MH, et al. (2014) Comparisons of Shewanella strains based on genome annotations, modeling, and experiments. BMC Syst Biol 8: 1–11. |
| iNJ661 | Jamshidi, Neema, and Bernhard Ø Palsson. Investigating the Metabolic Capabilities of Mycobacterium Tuberculosis H37Rv Using the in Silico Strain INJ661 and Proposing Alternative Drug Targets. BMC Systems Biology BMC Syst Biol: 26. |
| iNJ661v | Fang X, Wallqvist A, Reifman J. Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis. BMC Syst Biol 2010, 4:160. |
| iNJ661m | Fang X, Wallqvist A, Reifman J. Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis. BMC Syst Biol 2010, 4:160. |
| iSyn731 | Saha R, Verseput AT, Berla BM, Mueller TJ, Pakrasi HB, et al. (2012) Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. PLoS One 7. https://doi.org/10.1371/journal.pone.0048285. |
| Model | Reference |
|---|---|
| recon2.04 | Virtual Metabolic Human. https://vmh.uni.lu/. Accessed October 9, 2015 from the page https://vmh.uni.lu/#downloadview using the link to https://vmh.uni.lu/files/Recon2.v04.mat_.zip. |