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joana_meta.tsv
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joana_meta.tsv
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Model iD Organism SBML BIOMASS_ID Experimental essentiality? Year Reference PMID Notes
iMM518 Methanococcus maripaludis S2 Biomodels Yes;http://www.pnas.org/content/110/12/4726.long 2014 N. Goyal et al. 24553424
iSyf715 Synechococcus elongatus PCC7942 Biomodels Yes 2014 Triana et al. 25141288
iCR744 Rhodoferax ferrireducens Cobra_git_repository 2009 Risso et al. 19772637
iCS291 Helicobacter pylori Cobra_git_repository YES 2002 Schilling et al. 12142428
iCS400 Haemophilus influenzae Cobra_git_repository YES 2000 Schilling et al. 10716908
iGB555 Neisseria meningitidis Cobra_git_repository 2007 Baart et al. 17617894 fixed_version_from_cobragit
iJL432 Clostridium acetobutylicum Cobra_git_repository 2008 Lee et al. 18758767
iJS747 Geobacter metallireducens Cobra_git_repository 2009 Sun et al. 19175927
iMA945 Salmonella typhimurium LT2 Cobra_git_repository Yes 2009 AbuOun et al. 19690172
iMH551 Staphylococcus aureus Cobra_git_repository Yes 2005 Heinemann et al. 16155945
iMO1056 Pseudomonas aeruginosa Cobra_git_repository Yes 2008 Oberhardt et al. 18192387
iMP429_fixed Streptococcus thermophilus Cobra_git_repository 2009 Pastink et al. 19346354
iRM588 Geobacter sulfurreducens Cobra_git_repository 2006 Mahadevan et al. 16461711
iRS605 Francisella tularensis Cobra_git_repository YES 2010 Raghunathan et al. 20731870 Fixed version from cobra_git
iSH335 Mannheimia succiniciproducens Cobra_git_repository 2004 Hong et al. 15378067 no detailed biomass!!
iSyn669 Synechocystis sp. Cobra_git_repository 2010 Montagud et al. 21083885
iTY425 Mannheimia succiniciproducens Cobra_git_repository 2007 Kim et al. 17405177 downloaded fixed version from cobragit
iVM679 Porphyromonas gingivalis Cobra_git_repository Yes 2009 Mazumdar et al. 18931137
iWZ663 Ketogulonicigenium vulgare WSH-001 Cobra_git_repository 2012 Zou et al. 22728423
iZM363 Zymomonas mobilis Cobra_git_repository 2011 Widiastuti et al. 20967753
iZmobMBEL601 Zymomonas mobilis Cobra_git_repository 2010 Lee et al. 21092328
iJC568 Prochlorococcus marinus strain MED4 http://biomet-toolbox.org/index.php?page=models-Prochlorococcus NA NA NA
iSB1139 Pseudomonas fluorescens SBW25 https://memosys.i-med.ac.at/MEMOSys/fileUpload/FileUpload.seam;jsessionid=941F89BC196A3C97E0A6DCCFE5A9CDBE?fileUploadId=35 2013 Borgos et al. 23497367
GSMN-TB Mycobacterium tuberculosis Optflux repository BIOMASSe YES 2007 Beste et al. 17521419
iAO358 Lactococcus lactis subsp. lactis Optflux repository R_BIOMass Textmining 2005 Oliveira et al. 15982422
iBif452 Bifidobacterium adolescentis L2-32 Optflux repository 2014 El-Semman et al. 24708835
iCac802 Clostridium acetobutylicum ATCC 825 Optflux repository 2014 Satyakam et al. 25379054
iCyc792 Cyanothece sp. PCC 7424 Optflux repository 2013 Mueller et al. 24369854
iCyh755 Cyanothece sp. PCC 8802 Optflux repository 2013 Mueller et al. 24369854
iCyj826 Cyanothece sp. PCC 7822 Optflux repository 2013 Mueller et al. 24369854
iCyn731 Cyanothece sp. PCC 7425 Optflux repository 2013 Mueller et al. 24369854
iCyp752 Cyanothece sp. PCC 8801 Optflux repository 2013 Mueller et al. 24369854
iFap484 Faecalibacterium prausnitzii A2-165 Optflux repository 2014 El-Semman et al. 24708835
iIB700 Streptomyces coelicolor A3(2) Optflux repository R786 Textmining 2005 Borodina et al. 15930493
iJP962 Pseudomonas putida str. KT2440 Optflux repository IR10389 2011 Oberhardt et al. 21483480
iMF721 Pseudoalteromonas haloplanktis TAC125 Optflux repository 2014 Fondi et al. 24889559
iMG746 Methanosarcina barkeri Optflux repository R_Mb_biomass_65 Gonnerman et al. 23420771
iMLTC806cdf Clostridium difficile 630 Optflux repository 2014 M. Larocque et al. 25315994
iNF518 Lactococcus lactis subsp. cremosis Optflux repository 2013 Flahaut et al. 23974365
iRR1083 Salmonella typhimurium LT2 Optflux repository R_ST_Biomass_Final Yes 2009 Raghunathan et al. 19356237
iTT548 Thermus thermophilus Optflux repository 2014 Lee et al. 24774833
iMA789 Streptomyces coelicolor A3(2) Optflux repository; other version fixed from cobragit R_protein Textmining 2010 Alam et al. 20338070
iAI558 Moorella thermoacetica paper 2015 Islam et al. 25994252
iCyt773 Cyanothece sp. ATCC 51142 paper 2012 Saha et al. 23133581
iEB458 Sodalis glossinidius paper 2012 Belda et al. 22292008
iEM439 Zymomonas mobilis paper 2016 Motamedian et al. 26883123
iJH728 Synechococcus sp. 7002 paper 2016 Henry et al. 27036328
iLca12A_640 Lactobacillus casei 12A paper 2014 Vinay-Lara et al. 25365062
iLca334_548 Lactobacillus casei ATCC 334 paper 2014 Vinay-Lara et al. 25365062
iMK1208 Streptomyces coelicolor A3(2) paper 2014 Kim et al. 24623710
iPB890 Pseudomonas stutzeri paper 2015 Babaei et al. 26302703
iRBaquifex Aquifex aeolicus paper 2014 Braakman and Smith 24516572
iSyn731 Synechocystis sp. PCC 6803 paper 2012 Saha et al. 23133581
iWX1009 Bacillus licheniformis paper 2016 Guo et al. 26776566
AbyMBEL891 Acinetobacter baumannii AYE R_R753 Yes 2010 Kim et al. 20094653
iAbaylyiV4 Acinetobacter baylyi R_PROTEINSYN_DASH_RXN YES 2008 Durot et al. 2008 18840283
iAI549 Dehalococcoides R_BIO_CBDB1_DM_855 2010 Islam et al. 20811585
iAK692 Spirulina platensis R_SP0694 2012 Klanchui et al. 22703714
iBsu1103 Bacillus subtilis rxn10201 YES 2009 Henry et al. 19555510
iBT721 Lactobacillus plantarum WCFS1 R_biomass_LPL60 2006 Teusink et al. 17062565
iBT721_v2 Lactobacillus plantarum WCFS1 2010 Goffin et al. 20865006 modified version from iBT721
iCA1273 Escherichia coli W R_Ec_biomass_iCA1273_core_59p81M 2011 Archer et al. 21208457
iCAC490 Clostridium acetobutylicum ATCC 824 2012 McAnulty et al. 22583864
iCce806 Cyanothece sp. ATCC 51142 r_PROTSYN_CN 2012 Vu et al. 22529767
iCG230 Blattabacterium cuenoti Bge R_BiomassPam 2012 González-Domenech et al. 22376077
iCG238 Blattabacterium cuenoti Pam R_BiomassBge 2012 González-Domenech et al. 22376077
iCM925 Clostridium beijerinckii R_biomass 2011 Milne et al. 21846360
iDsh827 Dinoroseobacter shibae 2013 Rex et al. 24098096
iGT196 Buchnera aphidicola VGRO 2009 Thomas et al. 19232131 cobra_git annotated as not solved
iHZ565 Sinorhizobium meliloti paper 2012 Zhao et al. 22319621
iJP815 Pseudomonas putida str. KT2440 Optflux repository 2008 Puchalka et al. 18974823
iJW145 Mycoplasma pneumoniae IR09909 Yes 2013 Wodke et al. 23549481
iKF1028 Burkholderia cenocepacia J2315 Optflux repository IR10490 Yes 2011 Fang et al. 21609491
iLCBaumannia Candidatus Baumannia cicadellinicola 2010 Cottret et al. 20838465
iLCSulcia Candidatus Sulcia muelleri 2010 Cottret et al. 20838465
iMB745 Methanosarcina acetivorans str. C2A R_overall 2012 Benedict et al. 22139506
iMP240 Blattabacterium cuenoti 2013 Ponce-de-Léon et al. 24176055
iMZ1055 Bacillus megaterium R_RxnBME1112 2013 Zou et al. 23454894
iNJ661m Mycobacterium tuberculosis R_biomass_Mtb_9_60atp_test_NOF Yes 2010 Fang et al. 21092312
iNJ661v Mycobacterium tuberculosis R_biomass_Mtb_9_60atp_test_NOF Yes 2010 Fang et al. 21092312
iOG654 Nathromonas pharaonis RM00001 2009 Gonzalez et al. 20543878
iPS189 Mycoplasma genitalium R_Biomass Yes 2009 Suthers et al. 19214212
iRP911 Methylobacterium extorquens AM1 BiomassSynthesis 2011 Peyraud et al. 22074569
iRsp1095 Rhodobacter sphaeroides 2.4.1 R_RXN1306 2011 Imam et al. 21777427
iRsp1140 Rhodobacter sphaeroides 2.4.1 2013 Imam et al. 24034347
iSM197 Buchnera aphidicola Biomodels 2011 MacDonald et al. 21392141
iSO783 Shewanella oneidensis R_SO_BiomassMacro_DM_noATP2 Yes 2010 Pinchuk et al. 20589080
iSR432 Clostridium thermocellum paper R_biomass_target 2010 Roberts et al. 20307315
iSS352 Xanthomonas campestris pv. campestris str. B100 R_biomass1 2013 Schatschneider et al. 23395674
iTZ479 Thermotoga maritima paper R_BiomassEcoli_TM 2009 Zhang et al. 19762644
iVS941 Methanosarcina acetivorans 2011 Kumar et al. 22139506
iVW583 Amycolatopsis balhimycina Optflux repository R_1301 2011 Vongsangnak et al. 22252737
Nmb_iTM560 Neisseria meningitidis R_Nm_biomass Textmining 2011 Mendum et al. 22208880
PpuMBEL1071 Pseudomonas putida str. KT2440 paper R_Biomass 2010 Sohn et al. 20540110
sMtb Mycobacterium tuberculosis Yes 2014 Rienksma et al. 25453232
STM_v1.0 Salmonella typhimurium LT2 R_biomass_iRR1083 Yes 2011 Thiele et al. 21244678
VvuMBEL943 Vibrio vulnificus R_R806 textmining 2011 Kim et al. 21245845
Fu et al. , Shastri and Morgan Synechocystis sp. no cannot be solved on cobragit; autotrophic growth has the most components but still lacks a.a.; Equation from http://onlinelibrary.wiley.com/doi/10.1021/bp050246d/full
iAH991 Bacteroides thetaiotaomicron NO
iAM388 Campylobacter jejuni subsp. jejuni NCTC 11168 NO
iAN818m Yersinia pestis NO Yes 2009 Navid and Almas
iAT841 Methylomicrobium buryatense no 2015 de la Torre et al.
iCC908 Salinispora tropica no 2015 Contador et al.
iCL2075 Saccharopolyspora erythraea NRRL23338 NO 2012 Licona-Cassani et al
iDL546 Staphylococcus aureus NO Yes 13 strains - several biomass formulations based on previous
iHN637 Clostridium ljungdahlii NO 2013 Harish Nagarajan et al. 2013
iJE296 Haemophilus influenzae Rd KW20 NO YES 1999 Edwards et al. 1999
iJE660 Escherichia coli str. K12 substr. MG1655 NO YES 2000 Edwards et al. 2000
iJL846 Lactobacillus casei LC2W NO 2015 Xu et al. 2015
iJM658 Corynebacterium glutamicum S9114 NO 2016 http://www.sciencedirect.com/science/article/pii/S0378111915011476
iJSPcarbinolicus Pelobacter carbinolicus DSM 2380 NO http://aem.asm.org/content/74/14/4277.full http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-4-174
IJSPpropionicus Pelobacter propionicus DSM 2379 NO http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-4-174
iKK446 Corynebacterium glutamicum ATCC 13032 NO 2009 Kjeldsen et al. 2009;cannot be solved on cobragit
iKY620 Arthrospira platensis NO 2015 Yoshikawa et al.
iMT1174 Rhodococcus jostii RHA1 no 2015 Tajparast and Frigon
iNV706 Enterococcus faecalis V583 no 2014 Veith et al. 2014
iOA584 Chromohalobacter salexigens NO 2011 Ates et al. 2011;cannot be solved on cobragit
iOGhalobac Halobacterium salinarum NO Gonzalez et al.
iOR450 Rhizobium etli no 2012 Resendis-Antonio et al.; not for biomass, nitrogen fixation
iPC1209 Pectobacterium carotovorum subsp. carotovorum PC1 no Cheng Wang et al. 2015
iPD702 Streptomyces lividans no 2012 D'Huys et al.
iRS474 Clostridium acetobutylicum NO 2008 Senger et al. 2008
iSA399 Rhodococcus erythropolis NO 2011 Mol Biosyst
iSyp611 Synechococcus sp. 7002 no 2013 Vu et al.
iTU515 Sulfolobus Solfataricus P2 no Ulas et al.
iTZ479_v2 Thermotoga maritima NO
iXW433 Gluconobacter oxydans no 2014 Wu et al.
iYLW1028 Actinoplanes sp. SE50/110 no 2015 Wang et al.
iYS432 Corynebacterium glutamicum NO 2009 Shinfuku et al. 2009;cannot be solved on cobragit
KoxGSC1457 Klebsiella oxytoca NO 2013 J. Park et al. 2013
Lee et al. Ralstonia eutropha no
RehMBEL1391 Ralstonia eutropha H16 no Park et al. 2007
Rokem et al. Micrococcus luteus NO
SPNV1.0 Saccharopolyspora spinosa NRRL 18395 no Wang et al. 2014
iWT236 Thermoanaerobacter tengcongensis NO; says yes on the paper, waiting 2013 Tong et al.
iJL480 Streptococcus pyogenes NO; WAITING FOR REPLY EMAIL 2016 Hendry et al.
iOR363 Rhizobium etli yes, but no biomass eq. Model for nitrogen fixation