{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Import models" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Import models from files" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The function :class:`~cameo.io.load_model` accepts a number of different input formats.\n", "\n", "1. [SBML](http://sbml.org/) (Systems Biology Markup Language).\n", "2. JSON\n", "3. Pickle (pickled models)\n", "4. Model identifiers (from the [BiGG Models](http://bigg.ucsd.edu))" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "less data/e_coli_core.xml" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "from cameo import load_model\n", "model = load_model('data/e_coli_core.xml')" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
Namee_coli_core
Memory address0x01102bfdd8
Number of metabolites72
Number of reactions95
Objective expression-1.0*Biomass_Ecoli_core_w_GAM_reverse_1a29b + 1.0*Biomass_Ecoli_core_w_GAM
Compartmentsextracellular space, cytosol
" ], "text/plain": [ "" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "model" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Import models from the internet" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "In the quick start [chapter](1-quick-start.ipynb) 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. " ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "from cameo import models" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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bigg_idgene_countmetabolite_countorganismreaction_count
0e_coli_core13772Escherichia coli str. K-12 substr. MG165595
1iAB_RBC_283346342Homo sapiens469
2iAF126012611668Escherichia coli str. K-12 substr. MG16552382
3iAF1260b12611668Escherichia coli str. K-12 substr. MG16552388
4iAF692692628Methanosarcina barkeri str. Fusaro690
5iAF9879871109Geobacter metallireducens GS-151285
6iAPECO1_131213131942Escherichia coli APEC O12735
7iAT_PLT_636636738Homo sapiens1008
8iB21_139713371943Escherichia coli BL21(DE3)2741
9iBWG_132913291949Escherichia coli BW29522741
10ic_130613071936Escherichia coli CFT0732726
11iCHOv117664456Cricetulus griseus6663
12iE2348C_128612871919Escherichia coli O127:H6 str. E2348/692703
13iEC042_131413141926Escherichia coli 0422714
14iEC55989_133013301953Escherichia coli 559892756
15iECABU_c132013201942Escherichia coli ABU 839722731
16iECB_132813291951Escherichia coli B str. REL6062748
17iECBD_135413541952Escherichia coli 'BL21-Gold(DE3)pLysS AG'2748
18iECD_139113331943Escherichia coli BL21(DE3)2741
19iECDH10B_136813271947Escherichia coli str. K-12 substr. DH10B2742
20iEcDH1_136313631949Escherichia coli DH12750
21iECDH1ME8569_143914391950Escherichia coli DH12755
22iEcE24377_134113411972Escherichia coli O139:H28 str. E24377A2763
23iECED1_128212791929Escherichia coli ED1a2706
24iECH74115_126212621918Escherichia coli O157:H7 str. EC41152694
25iEcHS_132013211963Escherichia coli HS2753
26iECIAI1_134313431968Escherichia coli IAI12765
27iECIAI39_132213211953Escherichia coli IAI392721
28iECNA114_130113011927Escherichia coli NA1142718
29iECO103_132613271958Escherichia coli O103:H2 str. 120092758
..................
54iLF82_130413021938Escherichia coli LF822726
55iLJ478482570Thermotoga maritima MSB8652
56iML151515161877Escherichia coli str. K-12 substr. MG16552712
57iMM141513752775Mus musculus3726
58iMM9049051226Saccharomyces cerevisiae S288C1577
59iND7507501059Saccharomyces cerevisiae S288C1266
60iNF517516650Lactococcus lactis subsp. cremoris MG1363754
61iNJ661661825Mycobacterium tuberculosis H37Rv1025
62iNRG857_131313111943Escherichia coli O83:H1 str. NRG 857C2735
63iPC8158151552Yersinia pestis CO921961
64iRC108010861706Chlamydomonas reinhardtii2191
65iS_118811881914Shigella flexneri 2a str. 2457T2619
66iSB619619655Staphylococcus aureus subsp. aureus N315743
67iSbBS512_114611471910Shigella boydii CDC 3083-942591
68iSBO_113411341908Shigella boydii Sb2272591
69iSDY_105910591888Shigella dysenteriae Sd1972539
70iSF_119511951917Shigella flexneri 2a str. 3012630
71iSFV_118411841917Shigella flexneri 5 str. 84012621
72iSFxv_117211691918Shigella flexneri 20020172638
73iSSON_124012401936Shigella sonnei Ss0462693
74iUMN146_132113191942Escherichia coli UM1462735
75iUMNK88_135313531969Escherichia coli UMNK882777
76iUTI89_131013101940Escherichia coli UTI892725
77iWFL_137213721973Escherichia coli W2782
78iY75_135713581953Escherichia coli str. K-12 substr. W31102759
79iYL122812291658Klebsiella pneumoniae subsp. pneumoniae MGH 785782262
80iYO844844990Bacillus subtilis subsp. subtilis str. 1681250
81iZ_130813081923Escherichia coli O157:H7 str. EDL9332721
82RECON119052766Homo sapiens3741
83STM_v1_012711802Salmonella enterica subsp. enterica serovar Ty...2545
\n", "

84 rows × 5 columns

\n", "
" ], "text/plain": [ " bigg_id gene_count metabolite_count \\\n", "0 e_coli_core 137 72 \n", "1 iAB_RBC_283 346 342 \n", "2 iAF1260 1261 1668 \n", "3 iAF1260b 1261 1668 \n", "4 iAF692 692 628 \n", "5 iAF987 987 1109 \n", "6 iAPECO1_1312 1313 1942 \n", "7 iAT_PLT_636 636 738 \n", "8 iB21_1397 1337 1943 \n", "9 iBWG_1329 1329 1949 \n", "10 ic_1306 1307 1936 \n", "11 iCHOv1 1766 4456 \n", "12 iE2348C_1286 1287 1919 \n", "13 iEC042_1314 1314 1926 \n", "14 iEC55989_1330 1330 1953 \n", "15 iECABU_c1320 1320 1942 \n", "16 iECB_1328 1329 1951 \n", "17 iECBD_1354 1354 1952 \n", "18 iECD_1391 1333 1943 \n", "19 iECDH10B_1368 1327 1947 \n", "20 iEcDH1_1363 1363 1949 \n", "21 iECDH1ME8569_1439 1439 1950 \n", "22 iEcE24377_1341 1341 1972 \n", "23 iECED1_1282 1279 1929 \n", "24 iECH74115_1262 1262 1918 \n", "25 iEcHS_1320 1321 1963 \n", "26 iECIAI1_1343 1343 1968 \n", "27 iECIAI39_1322 1321 1953 \n", "28 iECNA114_1301 1301 1927 \n", "29 iECO103_1326 1327 1958 \n", ".. ... ... ... \n", "54 iLF82_1304 1302 1938 \n", "55 iLJ478 482 570 \n", "56 iML1515 1516 1877 \n", "57 iMM1415 1375 2775 \n", "58 iMM904 905 1226 \n", "59 iND750 750 1059 \n", "60 iNF517 516 650 \n", "61 iNJ661 661 825 \n", "62 iNRG857_1313 1311 1943 \n", "63 iPC815 815 1552 \n", "64 iRC1080 1086 1706 \n", "65 iS_1188 1188 1914 \n", "66 iSB619 619 655 \n", "67 iSbBS512_1146 1147 1910 \n", "68 iSBO_1134 1134 1908 \n", "69 iSDY_1059 1059 1888 \n", "70 iSF_1195 1195 1917 \n", "71 iSFV_1184 1184 1917 \n", "72 iSFxv_1172 1169 1918 \n", "73 iSSON_1240 1240 1936 \n", "74 iUMN146_1321 1319 1942 \n", "75 iUMNK88_1353 1353 1969 \n", "76 iUTI89_1310 1310 1940 \n", "77 iWFL_1372 1372 1973 \n", "78 iY75_1357 1358 1953 \n", "79 iYL1228 1229 1658 \n", "80 iYO844 844 990 \n", "81 iZ_1308 1308 1923 \n", "82 RECON1 1905 2766 \n", "83 STM_v1_0 1271 1802 \n", "\n", " organism reaction_count \n", "0 Escherichia coli str. K-12 substr. MG1655 95 \n", "1 Homo sapiens 469 \n", "2 Escherichia coli str. K-12 substr. MG1655 2382 \n", "3 Escherichia coli str. K-12 substr. MG1655 2388 \n", "4 Methanosarcina barkeri str. Fusaro 690 \n", "5 Geobacter metallireducens GS-15 1285 \n", "6 Escherichia coli APEC O1 2735 \n", "7 Homo sapiens 1008 \n", "8 Escherichia coli BL21(DE3) 2741 \n", "9 Escherichia coli BW2952 2741 \n", "10 Escherichia coli CFT073 2726 \n", "11 Cricetulus griseus 6663 \n", "12 Escherichia coli O127:H6 str. E2348/69 2703 \n", "13 Escherichia coli 042 2714 \n", "14 Escherichia coli 55989 2756 \n", "15 Escherichia coli ABU 83972 2731 \n", "16 Escherichia coli B str. REL606 2748 \n", "17 Escherichia coli 'BL21-Gold(DE3)pLysS AG' 2748 \n", "18 Escherichia coli BL21(DE3) 2741 \n", "19 Escherichia coli str. K-12 substr. DH10B 2742 \n", "20 Escherichia coli DH1 2750 \n", "21 Escherichia coli DH1 2755 \n", "22 Escherichia coli O139:H28 str. E24377A 2763 \n", "23 Escherichia coli ED1a 2706 \n", "24 Escherichia coli O157:H7 str. EC4115 2694 \n", "25 Escherichia coli HS 2753 \n", "26 Escherichia coli IAI1 2765 \n", "27 Escherichia coli IAI39 2721 \n", "28 Escherichia coli NA114 2718 \n", "29 Escherichia coli O103:H2 str. 12009 2758 \n", ".. ... ... \n", "54 Escherichia coli LF82 2726 \n", "55 Thermotoga maritima MSB8 652 \n", "56 Escherichia coli str. K-12 substr. MG1655 2712 \n", "57 Mus musculus 3726 \n", "58 Saccharomyces cerevisiae S288C 1577 \n", "59 Saccharomyces cerevisiae S288C 1266 \n", "60 Lactococcus lactis subsp. cremoris MG1363 754 \n", "61 Mycobacterium tuberculosis H37Rv 1025 \n", "62 Escherichia coli O83:H1 str. NRG 857C 2735 \n", "63 Yersinia pestis CO92 1961 \n", "64 Chlamydomonas reinhardtii 2191 \n", "65 Shigella flexneri 2a str. 2457T 2619 \n", "66 Staphylococcus aureus subsp. aureus N315 743 \n", "67 Shigella boydii CDC 3083-94 2591 \n", "68 Shigella boydii Sb227 2591 \n", "69 Shigella dysenteriae Sd197 2539 \n", "70 Shigella flexneri 2a str. 301 2630 \n", "71 Shigella flexneri 5 str. 8401 2621 \n", "72 Shigella flexneri 2002017 2638 \n", "73 Shigella sonnei Ss046 2693 \n", "74 Escherichia coli UM146 2735 \n", "75 Escherichia coli UMNK88 2777 \n", "76 Escherichia coli UTI89 2725 \n", "77 Escherichia coli W 2782 \n", "78 Escherichia coli str. K-12 substr. W3110 2759 \n", "79 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 2262 \n", "80 Bacillus subtilis subsp. subtilis str. 168 1250 \n", "81 Escherichia coli O157:H7 str. EDL933 2721 \n", "82 Homo sapiens 3741 \n", "83 Salmonella enterica subsp. enterica serovar Ty... 2545 \n", "\n", "[84 rows x 5 columns]" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "models.index_models_bigg()" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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idnamedoiauthoryearformatsorganismtaxonomyvalidated
01iJR90410.1186/gb-2003-4-9-r54Reed2003[sbml]Escherichia coli str. K12 substr. MG1655Bacteria; Proteobacteria; Gammaproteobacteria;...True
12iAF126010.1038/msb4100155Feist2007[sbml]Escherichia coli str. K12 substr. MG1655Bacteria; Proteobacteria; Gammaproteobacteria;...True
23iMM90410.1186/1752-0509-3-37Mo2007[sbml]Saccharomyces cerevisiaeEukaryota; Opisthokonta; Fungi; Dikarya; Ascom...True
34iJP81510.1371/journal.pcbi.1000210Puchalka2008[sbml]Pseudomonas putida str. KT2440Bacteria; Proteobacteria; Gammaproteobacteria;...True
45iMO105610.1128/JB.01583-07Oberhardt2008[excel]Pseudomonas aeruginosa str. PAO1Bacteria; Proteobacteria; Gammaproteobacteria;...False
56iIN80010.1186/1752-0509-2-71Nookaew2008[sbml]Saccharomyces cerevisiaeEukaryota; Opisthokonta; Fungi; Dikarya; Ascom...False
67iFF70810.1101/gr.234503Förster2003[sbml]Saccharomyces cerevisiae str. Sc288Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom...False
78iCA127310.1186/1471-2164-12-9Archer2011[sbml]Escherichia coli WBacteria; Proteobacteria; Gammaproteobacteria;...True
89iJO136610.1038/msb.2011.65Orth2011[sbml]Escherichia coli str. K12 substr. MG1655Bacteria; Proteobacteria; Gammaproteobacteria;...True
910yeast 4.010.1186/1752-0509-4-145Dobson2010[]YeastEukaryota; Opisthokonta; Fungi;False
1011iJN74610.1186/1752-0509-2-79Nogales2008[sbml]Pseudomonas putida str. KT2440Bacteria; Proteobacteria; Gammaproteobacteria;...True
1112AbyMBEL89110.1039/B916446DKim2010[sbml]Acinetobacter baumannii AYEBacteria; Proteobacteria; Gammaproteobacteria;...False
1213iJP96210.1371/journal.pcbi.1001116Oberhardt2011[sbml]Pseudomonas putida str. KT2440Bacteria; Proteobacteria; Gammaproteobacteria;...True
1314iYL122810.1128/JB.01218-10Liao2011[sbml]Klebsiella pneumoniae str. MGH 78578Bacteria; Proteobacteria; Gammaproteobacteria;...True
1415iSR43210.1186/1752-0509-4-31Roberts2010[sbml]Clostridium thermocellum str. ATCC 27405Bacteria; Firmicutes; Clostridia; Clostridial...True
1516iNJ661m10.1186/1752-0509-4-160Fang2010[sbml]Mycobacterium tuberculosis str. H37RvBacteria; Actinobacteria; Actinobacteria; Acti...True
1617iCM92510.1186/1752-0509-5-130Milne2011[sbml]Clostridium beijerinckii str. NCIMB 8052Bacteria; Firmicutes; Clostridia; Clostridiale...True
1718iBsu110310.1186/gb-2009-10-6-r69Henry2009[sbml]Bacillus subtilis 168Bacteria; Firmicutes; Bacilli; Bacillales; Bac...True
1819iAI54910.1371/journal.pcbi.1000887Islam2010[sbml]Dehalococcoides ethenogenes str. 2061Bacteria; Chloroflexi; Dehalococcoidetes; Deha...True
1920iAF69210.1038/msb4100046Feist2006[sbml]Methanosarcina barkeriArchaea; Euryarchaeota; Methanomicrobia; Metha...True
2021AraGEM10.1186/1471-2164-12-S4-S5de Oliveira Dal'Molin2010[sbml]Arabidopsis thalianaEukaryota; Viridiplantae; Streptophyta; Strept...True
2122Ecoli core Modeldoi:10.1128/ecosalplus.10.2.1Orth2010[sbml]Escherichia coli str. K12 substr. MG1655Bacteria; Proteobacteria; Gammaproteobacteria;...True
2223iIT34110.1128/JB.187.16.5818-5830.2005Thiele2005[sbml]Helicobacter pylori str. 26695Bacteria; Proteobacteria; delta/epsilon subdi...True
2324iMH805/77510.1038/nbt1492Herrgård2008[sbml]Saccharomyces cerevisiae str. Sc288Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom...False
2425iND75010.1101/gr.2250904Duarte2004[sbml]Saccharomyces cerevisiae str. Sc288Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom...True
2526iRC108010.1038/msb.2011.52Chang2011[sbml]Chlamydomonas reinhardtiiEukaryota; Viridiplantae; Chlorophyta; Chlorop...True
2627iSB61910.1186/1471-2180-5-8Becker2005[sbml]Staphylococcus aureusBacteria; Firmicutes; Bacilli; Bacillales; St...True
2728iTH36610.1038/msb.2010.60Plata2010[sbml]Plasmodium falciparumEukaryota; Alveolata; Apicomplexa; Aconoidasid...True
2829iTZ47910.1126/science.1174671Zhang2009[sbml]Thermotoga maritima str. MSB8Bacteria; Thermotogae; Thermotogae; Thermotoga...True
2930recon210.1038/nbt.2488Thiele2013[sbml]Homo sapiensEukaryota; Opisthokonta; Metazoa; Eumetazoa; B...True
..............................
118123iCyc79210.1186/1752-0509-7-142Mueller2013[sbml, excel]Cyanothece sp. PCC 7424Bacteria; Cyanobacteria; Oscillatoriophycideae...False
119124iCyn73110.1186/1752-0509-7-142Mueller2013[sbml, excel]Cyanothece sp. PCC 7425Bacteria; Cyanobacteria; Oscillatoriophycideae...False
120125iCyj82610.1186/1752-0509-7-142Mueller2013[sbml, excel]Cyanothece sp. PCC 7822Bacteria; Cyanobacteria; Oscillatoriophycideae...False
121126iCyp75210.1186/1752-0509-7-142Mueller2013[sbml, excel]Cyanothece sp. PCC 8801Bacteria; Cyanobacteria; Oscillatoriophycideae...False
122127iCyh75510.1186/1752-0509-7-142Mueller2013[sbml, excel]Cyanothece sp. PCC 8802Bacteria; Cyanobacteria; Oscillatoriophycideae...False
123128iNF51810.1007/s00253-013-5140-2Flahaut2013[sbml]Lactococcus lactis subsp. cremoris MG1363Bacteria; Firmicutes; Bacilli; Lactobacillales...True
124129iJL145410.1039/C3MB70090AJie Liu2013[excel]Aspergillus terreus NIH2624Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom...False
125130iBif45210.1186/1752-0509-8-41El-Semman2014[sbml, excel]Bifidobacterium adolescentis L2-32Bacteria; Actinobacteria; Actinobacteria; Acti...False
126131iFap48410.1186/1752-0509-8-41El-Semman2014[sbml, excel]Faecalibacterium prausnitzii A2-165Bacteria; Firmicutes; Clostridia; Clostridiale...False
127132iAM38810.1186/1471-2164-12-535Aline Metris2011[excel]Campylobacter jejuni subsp. jejuni NCTC 11168Bacteria; Proteobacteria; delta/epsilon subdiv...False
128133iTT54810.1186/1475-2859-13-61Na-Rae Lee2014[sbml, excel]Thermus thermophilusBacteria; Deinococcus-Thermus; Deinococci; The...True
129134EctoGEM-1.010.1111/tpj.12627Prigent2014[sbml]Ectocarpus siliculosusEukaryota; Stramenopiles; PX clade; Phaeophyce...False
130135iMF72110.1111/1462-2920.12513Fondi2014[sbml]Pseudoalteromonas haloplanktis TAC125Bacteria; Proteobacteria; Gammaproteobacteria;...False
131136Arabidopsis core model10.1104/pp.114.235358Arnold2014[sbml]Arabidopsis thalianaEukaryota; Viridiplantae; Streptophyta; Strept...False
132137iHN63710.1186/1475-2859-12-118Harish Nagarajan2013[excel]Clostridium ljungdahliiBacteria; Firmicutes; Clostridia; Clostridiale...False
133138iCac80210.1186/s13068-014-0144-4Satyakam Dash2014[sbml]Clostridium acetobutylicum ATCC 824Bacteria; Firmicutes; Clostridia; Clostridiale...True
134139iMLTC806cdf10.1186/s12918-014-0117-zM. Larocque2014[sbml, excel]Clostridium difficile 630Bacteria; Firmicutes; Clostridia; Clostridiale...True
135140iCY110610.1186/s12918-014-0137-8Chao Ye2015[sbml]Mortierella alpinaEukaryota; Opisthokonta; Fungi; Fungi incertae...False
136141iMM51810.1039/c3mb70421aN. Goyal2014[excel]Methanococcus maripaludis S2Archaea; Euryarchaeota; Methanococci; Methanoc...False
137142iPC120910.1016/j.febslet.2014.12.010Cheng Wang2015[]Pectobacterium carotovorum subsp. carotovorum PC1Bacteria; Proteobacteria; Gammaproteobacteria;...False
138143iNV70610.1128/AEM.03279-14N. Veith2014[]Enterococcus faecalis V583Bacteria; Firmicutes; Bacilli; Lactobacillales...False
139144KoxGSC145710.1186/1475-2859-12-20J. Park2013[]Klebsiella oxytocaBacteria; Proteobacteria; Gammaproteobacteria;...False
140145iJL84610.1016/j.gene.2014.10.034Jie Liu2015[]Lactobacillus casei LC2WBacteria; Firmicutes; Bacilli; Lactobacillales...False
141146yeast 7.610.1089/ind.2013.0013Aung (updated)2015[sbml]YeastEukaryota; Opisthokonta; Fungi;False
142147iJK84910.1111/tpj.13081Joomi Kim2015[sbml, excel]Phaeodactylum tricornutumEukaryota; Stramenopiles; Bacillariophyta; Bac...True
143148iNL89510.1186/1752-0509-6-35Nicolas Loira2012[sbml]Yarrowia lipolyticaEukaryota; Fungi; Dikarya; Ascomycota; Sacchar...False
144149iYali410.1038/npjsba.2016.5Kerkhoven2016[sbml]Yarrowia lipolyticaEukaryota; Fungi; Dikarya; Ascomycota; Sacchar...False
145150iLB1027_lipid10.1371/journal.pone.0155038Jennifer Levering2016[sbml]Phaeodactylum tricornutumEukaryota; Stramenopiles; Bacillariophyta; Bac...True
146151iLB102710.1371/journal.pone.0155038Jennifer Levering2016[sbml]Phaeodactylum tricornutumEukaryota; Stramenopiles; Bacillariophyta; Bac...True
147152iMT117410.1186/s12918-015-0190-yMohammad Tajparast2015[excel]Rhodococcus jostii RHA1Bacteria; Terrabacteria group; Actinobacteria;...False
\n", "

148 rows × 9 columns

\n", "
" ], "text/plain": [ " id name doi \\\n", "0 1 iJR904 10.1186/gb-2003-4-9-r54 \n", "1 2 iAF1260 10.1038/msb4100155 \n", "2 3 iMM904 10.1186/1752-0509-3-37 \n", "3 4 iJP815 10.1371/journal.pcbi.1000210 \n", "4 5 iMO1056 10.1128/JB.01583-07 \n", "5 6 iIN800 10.1186/1752-0509-2-71 \n", "6 7 iFF708 10.1101/gr.234503 \n", "7 8 iCA1273 10.1186/1471-2164-12-9 \n", "8 9 iJO1366 10.1038/msb.2011.65 \n", "9 10 yeast 4.0 10.1186/1752-0509-4-145 \n", "10 11 iJN746 10.1186/1752-0509-2-79 \n", "11 12 AbyMBEL891 10.1039/B916446D \n", "12 13 iJP962 10.1371/journal.pcbi.1001116 \n", "13 14 iYL1228 10.1128/JB.01218-10 \n", "14 15 iSR432 10.1186/1752-0509-4-31 \n", "15 16 iNJ661m 10.1186/1752-0509-4-160 \n", "16 17 iCM925 10.1186/1752-0509-5-130 \n", "17 18 iBsu1103 10.1186/gb-2009-10-6-r69 \n", "18 19 iAI549 10.1371/journal.pcbi.1000887 \n", "19 20 iAF692 10.1038/msb4100046 \n", "20 21 AraGEM 10.1186/1471-2164-12-S4-S5 \n", "21 22 Ecoli core Model doi:10.1128/ecosalplus.10.2.1 \n", "22 23 iIT341 10.1128/JB.187.16.5818-5830.2005 \n", "23 24 iMH805/775 10.1038/nbt1492 \n", "24 25 iND750 10.1101/gr.2250904 \n", "25 26 iRC1080 10.1038/msb.2011.52 \n", "26 27 iSB619 10.1186/1471-2180-5-8 \n", "27 28 iTH366 10.1038/msb.2010.60 \n", "28 29 iTZ479 10.1126/science.1174671 \n", "29 30 recon2 10.1038/nbt.2488 \n", ".. ... ... ... \n", "118 123 iCyc792 10.1186/1752-0509-7-142 \n", "119 124 iCyn731 10.1186/1752-0509-7-142 \n", "120 125 iCyj826 10.1186/1752-0509-7-142 \n", "121 126 iCyp752 10.1186/1752-0509-7-142 \n", "122 127 iCyh755 10.1186/1752-0509-7-142 \n", "123 128 iNF518 10.1007/s00253-013-5140-2 \n", "124 129 iJL1454 10.1039/C3MB70090A \n", "125 130 iBif452 10.1186/1752-0509-8-41 \n", "126 131 iFap484 10.1186/1752-0509-8-41 \n", "127 132 iAM388 10.1186/1471-2164-12-535 \n", "128 133 iTT548 10.1186/1475-2859-13-61 \n", "129 134 EctoGEM-1.0 10.1111/tpj.12627 \n", "130 135 iMF721 10.1111/1462-2920.12513 \n", "131 136 Arabidopsis core model 10.1104/pp.114.235358 \n", "132 137 iHN637 10.1186/1475-2859-12-118 \n", "133 138 iCac802 10.1186/s13068-014-0144-4 \n", "134 139 iMLTC806cdf 10.1186/s12918-014-0117-z \n", "135 140 iCY1106 10.1186/s12918-014-0137-8 \n", "136 141 iMM518 10.1039/c3mb70421a \n", "137 142 iPC1209 10.1016/j.febslet.2014.12.010 \n", "138 143 iNV706 10.1128/AEM.03279-14 \n", "139 144 KoxGSC1457 10.1186/1475-2859-12-20 \n", "140 145 iJL846 10.1016/j.gene.2014.10.034 \n", "141 146 yeast 7.6 10.1089/ind.2013.0013 \n", "142 147 iJK849 10.1111/tpj.13081 \n", "143 148 iNL895 10.1186/1752-0509-6-35 \n", "144 149 iYali4 10.1038/npjsba.2016.5 \n", "145 150 iLB1027_lipid 10.1371/journal.pone.0155038 \n", "146 151 iLB1027 10.1371/journal.pone.0155038 \n", "147 152 iMT1174 10.1186/s12918-015-0190-y \n", "\n", " author year formats \\\n", "0 Reed 2003 [sbml] \n", "1 Feist 2007 [sbml] \n", "2 Mo 2007 [sbml] \n", "3 Puchalka 2008 [sbml] \n", "4 Oberhardt 2008 [excel] \n", "5 Nookaew 2008 [sbml] \n", "6 Förster 2003 [sbml] \n", "7 Archer 2011 [sbml] \n", "8 Orth 2011 [sbml] \n", "9 Dobson 2010 [] \n", "10 Nogales 2008 [sbml] \n", "11 Kim 2010 [sbml] \n", "12 Oberhardt 2011 [sbml] \n", "13 Liao 2011 [sbml] \n", "14 Roberts 2010 [sbml] \n", "15 Fang 2010 [sbml] \n", "16 Milne 2011 [sbml] \n", "17 Henry 2009 [sbml] \n", "18 Islam 2010 [sbml] \n", "19 Feist 2006 [sbml] \n", "20 de Oliveira Dal'Molin 2010 [sbml] \n", "21 Orth 2010 [sbml] \n", "22 Thiele 2005 [sbml] \n", "23 Herrgård 2008 [sbml] \n", "24 Duarte 2004 [sbml] \n", "25 Chang 2011 [sbml] \n", "26 Becker 2005 [sbml] \n", "27 Plata 2010 [sbml] \n", "28 Zhang 2009 [sbml] \n", "29 Thiele 2013 [sbml] \n", ".. ... ... ... \n", "118 Mueller 2013 [sbml, excel] \n", "119 Mueller 2013 [sbml, excel] \n", "120 Mueller 2013 [sbml, excel] \n", "121 Mueller 2013 [sbml, excel] \n", "122 Mueller 2013 [sbml, excel] \n", "123 Flahaut 2013 [sbml] \n", "124 Jie Liu 2013 [excel] \n", "125 El-Semman 2014 [sbml, excel] \n", "126 El-Semman 2014 [sbml, excel] \n", "127 Aline Metris 2011 [excel] \n", "128 Na-Rae Lee 2014 [sbml, excel] \n", "129 Prigent 2014 [sbml] \n", "130 Fondi 2014 [sbml] \n", "131 Arnold 2014 [sbml] \n", "132 Harish Nagarajan 2013 [excel] \n", "133 Satyakam Dash 2014 [sbml] \n", "134 M. Larocque 2014 [sbml, excel] \n", "135 Chao Ye 2015 [sbml] \n", "136 N. Goyal 2014 [excel] \n", "137 Cheng Wang 2015 [] \n", "138 N. Veith 2014 [] \n", "139 J. Park 2013 [] \n", "140 Jie Liu 2015 [] \n", "141 Aung (updated) 2015 [sbml] \n", "142 Joomi Kim 2015 [sbml, excel] \n", "143 Nicolas Loira 2012 [sbml] \n", "144 Kerkhoven 2016 [sbml] \n", "145 Jennifer Levering 2016 [sbml] \n", "146 Jennifer Levering 2016 [sbml] \n", "147 Mohammad Tajparast 2015 [excel] \n", "\n", " organism \\\n", "0 Escherichia coli str. K12 substr. MG1655 \n", "1 Escherichia coli str. K12 substr. MG1655 \n", "2 Saccharomyces cerevisiae \n", "3 Pseudomonas putida str. KT2440 \n", "4 Pseudomonas aeruginosa str. PAO1 \n", "5 Saccharomyces cerevisiae \n", "6 Saccharomyces cerevisiae str. Sc288 \n", "7 Escherichia coli W \n", "8 Escherichia coli str. K12 substr. MG1655 \n", "9 Yeast \n", "10 Pseudomonas putida str. KT2440 \n", "11 Acinetobacter baumannii AYE \n", "12 Pseudomonas putida str. KT2440 \n", "13 Klebsiella pneumoniae str. MGH 78578 \n", "14 Clostridium thermocellum str. ATCC 27405 \n", "15 Mycobacterium tuberculosis str. H37Rv \n", "16 Clostridium beijerinckii str. NCIMB 8052 \n", "17 Bacillus subtilis 168 \n", "18 Dehalococcoides ethenogenes str. 2061 \n", "19 Methanosarcina barkeri \n", "20 Arabidopsis thaliana \n", "21 Escherichia coli str. K12 substr. MG1655 \n", "22 Helicobacter pylori str. 26695 \n", "23 Saccharomyces cerevisiae str. Sc288 \n", "24 Saccharomyces cerevisiae str. Sc288 \n", "25 Chlamydomonas reinhardtii \n", "26 Staphylococcus aureus \n", "27 Plasmodium falciparum \n", "28 Thermotoga maritima str. MSB8 \n", "29 Homo sapiens \n", ".. ... \n", "118 Cyanothece sp. PCC 7424 \n", "119 Cyanothece sp. PCC 7425 \n", "120 Cyanothece sp. PCC 7822 \n", "121 Cyanothece sp. PCC 8801 \n", "122 Cyanothece sp. PCC 8802 \n", "123 Lactococcus lactis subsp. cremoris MG1363 \n", "124 Aspergillus terreus NIH2624 \n", "125 Bifidobacterium adolescentis L2-32 \n", "126 Faecalibacterium prausnitzii A2-165 \n", "127 Campylobacter jejuni subsp. jejuni NCTC 11168 \n", "128 Thermus thermophilus \n", "129 Ectocarpus siliculosus \n", "130 Pseudoalteromonas haloplanktis TAC125 \n", "131 Arabidopsis thaliana \n", "132 Clostridium ljungdahlii \n", "133 Clostridium acetobutylicum ATCC 824 \n", "134 Clostridium difficile 630 \n", "135 Mortierella alpina \n", "136 Methanococcus maripaludis S2 \n", "137 Pectobacterium carotovorum subsp. carotovorum PC1 \n", "138 Enterococcus faecalis V583 \n", "139 Klebsiella oxytoca \n", "140 Lactobacillus casei LC2W \n", "141 Yeast \n", "142 Phaeodactylum tricornutum \n", "143 Yarrowia lipolytica \n", "144 Yarrowia lipolytica \n", "145 Phaeodactylum tricornutum \n", "146 Phaeodactylum tricornutum \n", "147 Rhodococcus jostii RHA1 \n", "\n", " taxonomy validated \n", "0 Bacteria; Proteobacteria; Gammaproteobacteria;... True \n", "1 Bacteria; Proteobacteria; Gammaproteobacteria;... True \n", "2 Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom... True \n", "3 Bacteria; Proteobacteria; Gammaproteobacteria;... True \n", "4 Bacteria; Proteobacteria; Gammaproteobacteria;... False \n", "5 Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom... False \n", "6 Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom... False \n", "7 Bacteria; Proteobacteria; Gammaproteobacteria;... True \n", "8 Bacteria; Proteobacteria; Gammaproteobacteria;... True \n", "9 Eukaryota; Opisthokonta; Fungi; False \n", "10 Bacteria; Proteobacteria; Gammaproteobacteria;... True \n", "11 Bacteria; Proteobacteria; Gammaproteobacteria;... False \n", "12 Bacteria; Proteobacteria; Gammaproteobacteria;... True \n", "13 Bacteria; Proteobacteria; Gammaproteobacteria;... True \n", "14 Bacteria; Firmicutes; Clostridia; Clostridial... True \n", "15 Bacteria; Actinobacteria; Actinobacteria; Acti... True \n", "16 Bacteria; Firmicutes; Clostridia; Clostridiale... True \n", "17 Bacteria; Firmicutes; Bacilli; Bacillales; Bac... True \n", "18 Bacteria; Chloroflexi; Dehalococcoidetes; Deha... True \n", "19 Archaea; Euryarchaeota; Methanomicrobia; Metha... True \n", "20 Eukaryota; Viridiplantae; Streptophyta; Strept... True \n", "21 Bacteria; Proteobacteria; Gammaproteobacteria;... True \n", "22 Bacteria; Proteobacteria; delta/epsilon subdi... True \n", "23 Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom... False \n", "24 Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom... True \n", "25 Eukaryota; Viridiplantae; Chlorophyta; Chlorop... True \n", "26 Bacteria; Firmicutes; Bacilli; Bacillales; St... True \n", "27 Eukaryota; Alveolata; Apicomplexa; Aconoidasid... True \n", "28 Bacteria; Thermotogae; Thermotogae; Thermotoga... True \n", "29 Eukaryota; Opisthokonta; Metazoa; Eumetazoa; B... True \n", ".. ... ... \n", "118 Bacteria; Cyanobacteria; Oscillatoriophycideae... False \n", "119 Bacteria; Cyanobacteria; Oscillatoriophycideae... False \n", "120 Bacteria; Cyanobacteria; Oscillatoriophycideae... False \n", "121 Bacteria; Cyanobacteria; Oscillatoriophycideae... False \n", "122 Bacteria; Cyanobacteria; Oscillatoriophycideae... False \n", "123 Bacteria; Firmicutes; Bacilli; Lactobacillales... True \n", "124 Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom... False \n", "125 Bacteria; Actinobacteria; Actinobacteria; Acti... False \n", "126 Bacteria; Firmicutes; Clostridia; Clostridiale... False \n", "127 Bacteria; Proteobacteria; delta/epsilon subdiv... False \n", "128 Bacteria; Deinococcus-Thermus; Deinococci; The... True \n", "129 Eukaryota; Stramenopiles; PX clade; Phaeophyce... False \n", "130 Bacteria; Proteobacteria; Gammaproteobacteria;... False \n", "131 Eukaryota; Viridiplantae; Streptophyta; Strept... False \n", "132 Bacteria; Firmicutes; Clostridia; Clostridiale... False \n", "133 Bacteria; Firmicutes; Clostridia; Clostridiale... True \n", "134 Bacteria; Firmicutes; Clostridia; Clostridiale... True \n", "135 Eukaryota; Opisthokonta; Fungi; Fungi incertae... False \n", "136 Archaea; Euryarchaeota; Methanococci; Methanoc... False \n", "137 Bacteria; Proteobacteria; Gammaproteobacteria;... False \n", "138 Bacteria; Firmicutes; Bacilli; Lactobacillales... False \n", "139 Bacteria; Proteobacteria; Gammaproteobacteria;... False \n", "140 Bacteria; Firmicutes; Bacilli; Lactobacillales... False \n", "141 Eukaryota; Opisthokonta; Fungi; False \n", "142 Eukaryota; Stramenopiles; Bacillariophyta; Bac... True \n", "143 Eukaryota; Fungi; Dikarya; Ascomycota; Sacchar... False \n", "144 Eukaryota; Fungi; Dikarya; Ascomycota; Sacchar... False \n", "145 Eukaryota; Stramenopiles; Bacillariophyta; Bac... True \n", "146 Eukaryota; Stramenopiles; Bacillariophyta; Bac... True \n", "147 Bacteria; Terrabacteria group; Actinobacteria;... False \n", "\n", "[148 rows x 9 columns]" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "models.index_models_minho()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Models from [BiGG](http://bigg.ucsd.edu) and the [University of Minho](http://darwin.di.uminho.pt/models) can conveniently be accessd via :class:`~cameo.models.bigg` and :class:`~cameo.models.minho` respectively." ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
NameiJN746
Memory address0x01106d16d8
Number of metabolites907
Number of reactions1054
Objective expression-1.0*BIOMASS_KT_TEMP_reverse_d18f7 + 1.0*BIOMASS_KT_TEMP
Compartmentsextracellular space, cytosol, periplasm
" ], "text/plain": [ "" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "models.bigg.iJN746" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
NameiMM904
Memory address0x0115e79a58
Number of metabolites1228
Number of reactions1577
Objective expression-1.0*biomass_SC5_notrace_reverse_e32ff + 1.0*biomass_SC5_notrace
CompartmentsGolgi_Apparatus, Extra_organism, Nucleus, Endoplasmic_Reticulum, Cytosol, Peroxisome, Mitochondria, Vacuole
" ], "text/plain": [ "" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "models.minho.iMM904" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "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." ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
NameHyunUkKim2010_VvuMBEL943_MetabolicModeling
Memory address0x010c1676a0
Number of metabolites912
Number of reactions1019
Objective expression0
Compartmentscell
" ], "text/plain": [ "" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "models.minho.validated.VvuMBEL943 # use TAB completion to see the other models" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "anaconda-cloud": {}, "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.2" } }, "nbformat": 4, "nbformat_minor": 4 }