The function ~cameo.io.load_model accepts a number of different input formats.
In [1]:
less data/e_coli_core.xml
In [2]:
from cameo import load_model
model = load_model('data/e_coli_core.xml')
In [3]:
model
Out[3]:
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 ~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.
In [4]:
from cameo import models
In [5]:
models.index_models_bigg()
Out[5]:
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
In [6]:
models.index_models_minho()
Out[6]:
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.
In [7]:
models.bigg.iJN746
Out[7]:
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
In [8]:
models.minho.iMM904
Out[8]:
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.
In [9]:
models.minho.validated.VvuMBEL943 # use TAB completion to see the other models
Out[9]:
Name
HyunUkKim2010_VvuMBEL943_MetabolicModeling
Memory address
0x010c1676a0
Number of metabolites
912
Number of reactions
1019
Objective expression
0
Compartments
cell
In [ ]:
Content source: biosustain/cameo-notebooks
Similar notebooks: