Collection of PSAMM metabolic models converted from publicly available models
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matlab/recon2.04
sbml
README.md

README.md

PSAMM model collection

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 Format Curations

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 References

Converted SBML Models

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.
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).
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.
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.
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.
iFF708 Forster, J. Genome-Scale Reconstruction of the Saccharomyces Cerevisiae Metabolic Network. Genome Research 13.2 (2003): 244-53. Web.
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
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.
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.
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.
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.
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.
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.

Converted Excel Models

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.

Converted MATLAB Models

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.