The function :class:~cameo.io.load_model
accepts a number of different input formats.
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 |
In the quick start chapter we demonstrated how to use :class:~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 :class:~cameo.models.bigg
and :class:~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 |