Import models

Import models from files

The function ~cameo.io.load_model accepts a number of different input formats.

  1. SBML (Systems Biology Markup Language).
  2. JSON
  3. Pickle (pickled models)
  4. Model identifiers (from the BiGG Models)
less data/e_coli_core.xml
from cameo import load_model
model = load_model('data/e_coli_core.xml')
model
Name e_coli_core
Memory address 0x01102bfdd8
Number of metabolites 72
Number of reactions 95
Objective expression -1.0*Biomass_Ecoli_core_w_GAM_reverse_1a29b + 1.0*Biomass_Ecoli_core_w_GAM
Compartments extracellular space, cytosol

Import models from the internet

In the quick start chapter we demonstrated how to use ~cameo.io.load_model to import a model by ID. But where did the model come from? Cameo has currently access to two model repositories on the internet, http://bigg.ucsd.edu and http://darwin.di.uminho.pt/models.

from cameo import models
models.index_models_bigg()
bigg_id gene_count metabolite_count organism reaction_count
0 e_coli_core 137 72 Escherichia coli str. K-12 substr. MG1655 95
1 iAB_RBC_283 346 342 Homo sapiens 469
2 iAF1260 1261 1668 Escherichia coli str. K-12 substr. MG1655 2382
3 iAF1260b 1261 1668 Escherichia coli str. K-12 substr. MG1655 2388
4 iAF692 692 628 Methanosarcina barkeri str. Fusaro 690
5 iAF987 987 1109 Geobacter metallireducens GS-15 1285
6 iAPECO1_1312 1313 1942 Escherichia coli APEC O1 2735
7 iAT_PLT_636 636 738 Homo sapiens 1008
8 iB21_1397 1337 1943 Escherichia coli BL21(DE3) 2741
9 iBWG_1329 1329 1949 Escherichia coli BW2952 2741
10 ic_1306 1307 1936 Escherichia coli CFT073 2726
11 iCHOv1 1766 4456 Cricetulus griseus 6663
12 iE2348C_1286 1287 1919 Escherichia coli O127:H6 str. E2348/69 2703
13 iEC042_1314 1314 1926 Escherichia coli 042 2714
14 iEC55989_1330 1330 1953 Escherichia coli 55989 2756
15 iECABU_c1320 1320 1942 Escherichia coli ABU 83972 2731
16 iECB_1328 1329 1951 Escherichia coli B str. REL606 2748
17 iECBD_1354 1354 1952 Escherichia coli 'BL21-Gold(DE3)pLysS AG' 2748
18 iECD_1391 1333 1943 Escherichia coli BL21(DE3) 2741
19 iECDH10B_1368 1327 1947 Escherichia coli str. K-12 substr. DH10B 2742
20 iEcDH1_1363 1363 1949 Escherichia coli DH1 2750
21 iECDH1ME8569_1439 1439 1950 Escherichia coli DH1 2755
22 iEcE24377_1341 1341 1972 Escherichia coli O139:H28 str. E24377A 2763
23 iECED1_1282 1279 1929 Escherichia coli ED1a 2706
24 iECH74115_1262 1262 1918 Escherichia coli O157:H7 str. EC4115 2694
25 iEcHS_1320 1321 1963 Escherichia coli HS 2753
26 iECIAI1_1343 1343 1968 Escherichia coli IAI1 2765
27 iECIAI39_1322 1321 1953 Escherichia coli IAI39 2721
28 iECNA114_1301 1301 1927 Escherichia coli NA114 2718
29 iECO103_1326 1327 1958 Escherichia coli O103:H2 str. 12009 2758
... ... ... ... ... ...
54 iLF82_1304 1302 1938 Escherichia coli LF82 2726
55 iLJ478 482 570 Thermotoga maritima MSB8 652
56 iML1515 1516 1877 Escherichia coli str. K-12 substr. MG1655 2712
57 iMM1415 1375 2775 Mus musculus 3726
58 iMM904 905 1226 Saccharomyces cerevisiae S288C 1577
59 iND750 750 1059 Saccharomyces cerevisiae S288C 1266
60 iNF517 516 650 Lactococcus lactis subsp. cremoris MG1363 754
61 iNJ661 661 825 Mycobacterium tuberculosis H37Rv 1025
62 iNRG857_1313 1311 1943 Escherichia coli O83:H1 str. NRG 857C 2735
63 iPC815 815 1552 Yersinia pestis CO92 1961
64 iRC1080 1086 1706 Chlamydomonas reinhardtii 2191
65 iS_1188 1188 1914 Shigella flexneri 2a str. 2457T 2619
66 iSB619 619 655 Staphylococcus aureus subsp. aureus N315 743
67 iSbBS512_1146 1147 1910 Shigella boydii CDC 3083-94 2591
68 iSBO_1134 1134 1908 Shigella boydii Sb227 2591
69 iSDY_1059 1059 1888 Shigella dysenteriae Sd197 2539
70 iSF_1195 1195 1917 Shigella flexneri 2a str. 301 2630
71 iSFV_1184 1184 1917 Shigella flexneri 5 str. 8401 2621
72 iSFxv_1172 1169 1918 Shigella flexneri 2002017 2638
73 iSSON_1240 1240 1936 Shigella sonnei Ss046 2693
74 iUMN146_1321 1319 1942 Escherichia coli UM146 2735
75 iUMNK88_1353 1353 1969 Escherichia coli UMNK88 2777
76 iUTI89_1310 1310 1940 Escherichia coli UTI89 2725
77 iWFL_1372 1372 1973 Escherichia coli W 2782
78 iY75_1357 1358 1953 Escherichia coli str. K-12 substr. W3110 2759
79 iYL1228 1229 1658 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 2262
80 iYO844 844 990 Bacillus subtilis subsp. subtilis str. 168 1250
81 iZ_1308 1308 1923 Escherichia coli O157:H7 str. EDL933 2721
82 RECON1 1905 2766 Homo sapiens 3741
83 STM_v1_0 1271 1802 Salmonella enterica subsp. enterica serovar Ty... 2545

84 rows × 5 columns

models.index_models_minho()
id name doi author year formats organism taxonomy validated
0 1 iJR904 10.1186/gb-2003-4-9-r54 Reed 2003 [sbml] Escherichia coli str. K12 substr. MG1655 Bacteria; Proteobacteria; Gammaproteobacteria;... True
1 2 iAF1260 10.1038/msb4100155 Feist 2007 [sbml] Escherichia coli str. K12 substr. MG1655 Bacteria; Proteobacteria; Gammaproteobacteria;... True
2 3 iMM904 10.1186/1752-0509-3-37 Mo 2007 [sbml] Saccharomyces cerevisiae Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom... True
3 4 iJP815 10.1371/journal.pcbi.1000210 Puchalka 2008 [sbml] Pseudomonas putida str. KT2440 Bacteria; Proteobacteria; Gammaproteobacteria;... True
4 5 iMO1056 10.1128/JB.01583-07 Oberhardt 2008 [excel] Pseudomonas aeruginosa str. PAO1 Bacteria; Proteobacteria; Gammaproteobacteria;... False
5 6 iIN800 10.1186/1752-0509-2-71 Nookaew 2008 [sbml] Saccharomyces cerevisiae Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom... False
6 7 iFF708 10.1101/gr.234503 Förster 2003 [sbml] Saccharomyces cerevisiae str. Sc288 Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom... False
7 8 iCA1273 10.1186/1471-2164-12-9 Archer 2011 [sbml] Escherichia coli W Bacteria; Proteobacteria; Gammaproteobacteria;... True
8 9 iJO1366 10.1038/msb.2011.65 Orth 2011 [sbml] Escherichia coli str. K12 substr. MG1655 Bacteria; Proteobacteria; Gammaproteobacteria;... True
9 10 yeast 4.0 10.1186/1752-0509-4-145 Dobson 2010 [] Yeast Eukaryota; Opisthokonta; Fungi; False
10 11 iJN746 10.1186/1752-0509-2-79 Nogales 2008 [sbml] Pseudomonas putida str. KT2440 Bacteria; Proteobacteria; Gammaproteobacteria;... True
11 12 AbyMBEL891 10.1039/B916446D Kim 2010 [sbml] Acinetobacter baumannii AYE Bacteria; Proteobacteria; Gammaproteobacteria;... False
12 13 iJP962 10.1371/journal.pcbi.1001116 Oberhardt 2011 [sbml] Pseudomonas putida str. KT2440 Bacteria; Proteobacteria; Gammaproteobacteria;... True
13 14 iYL1228 10.1128/JB.01218-10 Liao 2011 [sbml] Klebsiella pneumoniae str. MGH 78578 Bacteria; Proteobacteria; Gammaproteobacteria;... True
14 15 iSR432 10.1186/1752-0509-4-31 Roberts 2010 [sbml] Clostridium thermocellum str. ATCC 27405 Bacteria; Firmicutes; Clostridia; Clostridial... True
15 16 iNJ661m 10.1186/1752-0509-4-160 Fang 2010 [sbml] Mycobacterium tuberculosis str. H37Rv Bacteria; Actinobacteria; Actinobacteria; Acti... True
16 17 iCM925 10.1186/1752-0509-5-130 Milne 2011 [sbml] Clostridium beijerinckii str. NCIMB 8052 Bacteria; Firmicutes; Clostridia; Clostridiale... True
17 18 iBsu1103 10.1186/gb-2009-10-6-r69 Henry 2009 [sbml] Bacillus subtilis 168 Bacteria; Firmicutes; Bacilli; Bacillales; Bac... True
18 19 iAI549 10.1371/journal.pcbi.1000887 Islam 2010 [sbml] Dehalococcoides ethenogenes str. 2061 Bacteria; Chloroflexi; Dehalococcoidetes; Deha... True
19 20 iAF692 10.1038/msb4100046 Feist 2006 [sbml] Methanosarcina barkeri Archaea; Euryarchaeota; Methanomicrobia; Metha... True
20 21 AraGEM 10.1186/1471-2164-12-S4-S5 de Oliveira Dal'Molin 2010 [sbml] Arabidopsis thaliana Eukaryota; Viridiplantae; Streptophyta; Strept... True
21 22 Ecoli core Model doi:10.1128/ecosalplus.10.2.1 Orth 2010 [sbml] Escherichia coli str. K12 substr. MG1655 Bacteria; Proteobacteria; Gammaproteobacteria;... True
22 23 iIT341 10.1128/JB.187.16.5818-5830.2005 Thiele 2005 [sbml] Helicobacter pylori str. 26695 Bacteria; Proteobacteria; delta/epsilon subdi... True
23 24 iMH805/775 10.1038/nbt1492 Herrgård 2008 [sbml] Saccharomyces cerevisiae str. Sc288 Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom... False
24 25 iND750 10.1101/gr.2250904 Duarte 2004 [sbml] Saccharomyces cerevisiae str. Sc288 Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom... True
25 26 iRC1080 10.1038/msb.2011.52 Chang 2011 [sbml] Chlamydomonas reinhardtii Eukaryota; Viridiplantae; Chlorophyta; Chlorop... True
26 27 iSB619 10.1186/1471-2180-5-8 Becker 2005 [sbml] Staphylococcus aureus Bacteria; Firmicutes; Bacilli; Bacillales; St... True
27 28 iTH366 10.1038/msb.2010.60 Plata 2010 [sbml] Plasmodium falciparum Eukaryota; Alveolata; Apicomplexa; Aconoidasid... True
28 29 iTZ479 10.1126/science.1174671 Zhang 2009 [sbml] Thermotoga maritima str. MSB8 Bacteria; Thermotogae; Thermotogae; Thermotoga... True
29 30 recon2 10.1038/nbt.2488 Thiele 2013 [sbml] Homo sapiens Eukaryota; Opisthokonta; Metazoa; Eumetazoa; B... True
... ... ... ... ... ... ... ... ... ...
118 123 iCyc792 10.1186/1752-0509-7-142 Mueller 2013 [sbml, excel] Cyanothece sp. PCC 7424 Bacteria; Cyanobacteria; Oscillatoriophycideae... False
119 124 iCyn731 10.1186/1752-0509-7-142 Mueller 2013 [sbml, excel] Cyanothece sp. PCC 7425 Bacteria; Cyanobacteria; Oscillatoriophycideae... False
120 125 iCyj826 10.1186/1752-0509-7-142 Mueller 2013 [sbml, excel] Cyanothece sp. PCC 7822 Bacteria; Cyanobacteria; Oscillatoriophycideae... False
121 126 iCyp752 10.1186/1752-0509-7-142 Mueller 2013 [sbml, excel] Cyanothece sp. PCC 8801 Bacteria; Cyanobacteria; Oscillatoriophycideae... False
122 127 iCyh755 10.1186/1752-0509-7-142 Mueller 2013 [sbml, excel] Cyanothece sp. PCC 8802 Bacteria; Cyanobacteria; Oscillatoriophycideae... False
123 128 iNF518 10.1007/s00253-013-5140-2 Flahaut 2013 [sbml] Lactococcus lactis subsp. cremoris MG1363 Bacteria; Firmicutes; Bacilli; Lactobacillales... True
124 129 iJL1454 10.1039/C3MB70090A Jie Liu 2013 [excel] Aspergillus terreus NIH2624 Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom... False
125 130 iBif452 10.1186/1752-0509-8-41 El-Semman 2014 [sbml, excel] Bifidobacterium adolescentis L2-32 Bacteria; Actinobacteria; Actinobacteria; Acti... False
126 131 iFap484 10.1186/1752-0509-8-41 El-Semman 2014 [sbml, excel] Faecalibacterium prausnitzii A2-165 Bacteria; Firmicutes; Clostridia; Clostridiale... False
127 132 iAM388 10.1186/1471-2164-12-535 Aline Metris 2011 [excel] Campylobacter jejuni subsp. jejuni NCTC 11168 Bacteria; Proteobacteria; delta/epsilon subdiv... False
128 133 iTT548 10.1186/1475-2859-13-61 Na-Rae Lee 2014 [sbml, excel] Thermus thermophilus Bacteria; Deinococcus-Thermus; Deinococci; The... True
129 134 EctoGEM-1.0 10.1111/tpj.12627 Prigent 2014 [sbml] Ectocarpus siliculosus Eukaryota; Stramenopiles; PX clade; Phaeophyce... False
130 135 iMF721 10.1111/1462-2920.12513 Fondi 2014 [sbml] Pseudoalteromonas haloplanktis TAC125 Bacteria; Proteobacteria; Gammaproteobacteria;... False
131 136 Arabidopsis core model 10.1104/pp.114.235358 Arnold 2014 [sbml] Arabidopsis thaliana Eukaryota; Viridiplantae; Streptophyta; Strept... False
132 137 iHN637 10.1186/1475-2859-12-118 Harish Nagarajan 2013 [excel] Clostridium ljungdahlii Bacteria; Firmicutes; Clostridia; Clostridiale... False
133 138 iCac802 10.1186/s13068-014-0144-4 Satyakam Dash 2014 [sbml] Clostridium acetobutylicum ATCC 824 Bacteria; Firmicutes; Clostridia; Clostridiale... True
134 139 iMLTC806cdf 10.1186/s12918-014-0117-z M. Larocque 2014 [sbml, excel] Clostridium difficile 630 Bacteria; Firmicutes; Clostridia; Clostridiale... True
135 140 iCY1106 10.1186/s12918-014-0137-8 Chao Ye 2015 [sbml] Mortierella alpina Eukaryota; Opisthokonta; Fungi; Fungi incertae... False
136 141 iMM518 10.1039/c3mb70421a N. Goyal 2014 [excel] Methanococcus maripaludis S2 Archaea; Euryarchaeota; Methanococci; Methanoc... False
137 142 iPC1209 10.1016/j.febslet.2014.12.010 Cheng Wang 2015 [] Pectobacterium carotovorum subsp. carotovorum PC1 Bacteria; Proteobacteria; Gammaproteobacteria;... False
138 143 iNV706 10.1128/AEM.03279-14 N. Veith 2014 [] Enterococcus faecalis V583 Bacteria; Firmicutes; Bacilli; Lactobacillales... False
139 144 KoxGSC1457 10.1186/1475-2859-12-20 J. Park 2013 [] Klebsiella oxytoca Bacteria; Proteobacteria; Gammaproteobacteria;... False
140 145 iJL846 10.1016/j.gene.2014.10.034 Jie Liu 2015 [] Lactobacillus casei LC2W Bacteria; Firmicutes; Bacilli; Lactobacillales... False
141 146 yeast 7.6 10.1089/ind.2013.0013 Aung (updated) 2015 [sbml] Yeast Eukaryota; Opisthokonta; Fungi; False
142 147 iJK849 10.1111/tpj.13081 Joomi Kim 2015 [sbml, excel] Phaeodactylum tricornutum Eukaryota; Stramenopiles; Bacillariophyta; Bac... True
143 148 iNL895 10.1186/1752-0509-6-35 Nicolas Loira 2012 [sbml] Yarrowia lipolytica Eukaryota; Fungi; Dikarya; Ascomycota; Sacchar... False
144 149 iYali4 10.1038/npjsba.2016.5 Kerkhoven 2016 [sbml] Yarrowia lipolytica Eukaryota; Fungi; Dikarya; Ascomycota; Sacchar... False
145 150 iLB1027_lipid 10.1371/journal.pone.0155038 Jennifer Levering 2016 [sbml] Phaeodactylum tricornutum Eukaryota; Stramenopiles; Bacillariophyta; Bac... True
146 151 iLB1027 10.1371/journal.pone.0155038 Jennifer Levering 2016 [sbml] Phaeodactylum tricornutum Eukaryota; Stramenopiles; Bacillariophyta; Bac... True
147 152 iMT1174 10.1186/s12918-015-0190-y Mohammad Tajparast 2015 [excel] Rhodococcus jostii RHA1 Bacteria; Terrabacteria group; Actinobacteria;... False

148 rows × 9 columns

Models from BiGG and the University of Minho can conveniently be accessd via ~cameo.models.bigg and ~cameo.models.minho respectively.

models.bigg.iJN746
Name iJN746
Memory address 0x01106d16d8
Number of metabolites 907
Number of reactions 1054
Objective expression -1.0*BIOMASS_KT_TEMP_reverse_d18f7 + 1.0*BIOMASS_KT_TEMP
Compartments extracellular space, cytosol, periplasm
models.minho.iMM904
Name iMM904
Memory address 0x0115e79a58
Number of metabolites 1228
Number of reactions 1577
Objective expression -1.0*biomass_SC5_notrace_reverse_e32ff + 1.0*biomass_SC5_notrace
Compartments Golgi_Apparatus, Extra_organism, Nucleus, Endoplasmic_Reticulum, Cytosol, Peroxisome, Mitochondria, Vacuole

Models in the Minho database have been manually verified. The subset of models shown bellow can be used to run simulations as described in the publications.

models.minho.validated.VvuMBEL943 # use TAB completion to see the other models
Name HyunUkKim2010_VvuMBEL943_MetabolicModeling
Memory address 0x010c1676a0
Number of metabolites 912
Number of reactions 1019
Objective expression 0
Compartments cell