Models imported from BioModels

BioModels database distributes curated models of biochemical and cellular systems. Currently, the models can be retrieved in the SBML L2V1 format. The conversion of BioModels into CSML allows researchers to reuse these models on the CSML supported platforms.

There are 56 models in the fifth release of BioModels database. The conversion is automatically done by using the SBML2CSML converter. The converted results are available to download in the CSML 1.9 and 3.0 formats within the two leftmost columns of each row. For your convenience, the dataset is provided locally under the terms of use of BioModels. Please click the model name which is linked to BioModels for the detailed information about each model. Three models did not convert properly because there are some units only allowed in SBML.

BioModels database

CSML 1.9CSML 3.0Converted
total elements
(Entity
/Process
/Connector)
BioModels ID
Model name
Publication ID
-BIOMD0000000001.xml
Edelstein1996_EPSP_AChEvent
PMID:8983160
120 (61/17/42)BIOMD0000000002.xml
Edelstein1996_EPSP_AChSpecies
PMID:8983160
37 (22/7/8)BIOMD0000000003.xml
Goldbeter1991_MinMitOscil
PMID:1833774
45 (26/7/12)BIOMD0000000004.xml
Goldbeter1991_MinMitOscil_ExplInact
PMID:1833774
52 (25/9/18)BIOMD0000000005.xml
Tyson1991_CellCycle_6var
PMID:1831270
19 (11/3/5)BIOMD0000000006.xml
Tyson1991_CellCycle_2var
PMID:1831270
185 (98/30/57)BIOMD0000000007.xml
Novak1997_CellCycle
PMID:9256450
71 (32/13/26)BIOMD0000000008.xml
Gardner1998_CellCycle_Goldbeter
PMID:9826676
155 (75/20/60)BIOMD0000000009.xml
Huang1996_MAPK_ultrasens
PMID:8816754
74 (39/10/25)BIOMD0000000010.xml
Kholodenko2000_MAPK_feedback
PMID:10712587
195 (75/30/90)BIOMD0000000011.xml
Levchenko2000_MAPK_noScaffold
PMID:10823939
78 (39/12/27)BIOMD0000000012.xml
Elowitz2000_Repressilator
PMID:10659856
239 (138/21/80)BIOMD0000000013.xml
Poolman2004_CalvinCycle
PMID:15073223
1659 (473/300/886)BIOMD0000000014.xml
Levchenko2000_MAPK_Scaffold
PMID:10823939
292 (148/37/107)BIOMD0000000015.xml
Curto1998_purineMetabol
PMID:9664759
65 (35/10/20)BIOMD0000000016.xml
Goldbeter1995_CircClock
PMID:8587874
169 (110/14/45)BIOMD0000000017.xml
Hoefnagel2002_PyruvateBranches
PMID:11932446
370 (175/47/148)BIOMD0000000018.xml
Morrison1989_FolateCycle
PMID:2732237
31 (23/4/4)BIOMD0000000020.xml
hodgkin-huxley squid-axon 1952
PMID:12991237
133 (70/24/39)BIOMD0000000021.xml
Leloup1999_CircClock
PMID:10366496
183 (95/32/56)BIOMD0000000022.xml
Ueda2001_CircClock
PMID:11403560
117 (81/11/25)BIOMD0000000023.xml
Rohwer2001_Sucrose
PMID:11513743
27 (15/4/8)BIOMD0000000024.xml
Scheper1999_CircClock
PMID:9870936
41 (21/8/12)BIOMD0000000025.xml
Smolen2002_CircClock
PMID:12414672
77 (39/10/28)BIOMD0000000026.xml
Markevich2004_MAPK_orderedElementary
PMID:14744999
39 (20/4/15)BIOMD0000000027.xml
Markevich2004_MAPK_orderedMM
PMID:14744999
125 (60/17/48)BIOMD0000000028.xml
Markevich2004_MAPK_phosphoRandomElementary
PMID:14744999
56 (28/7/21)BIOMD0000000029.xml
Markevich2004_MAPK_phosphoRandomMM
PMID:14744999
145 (69/20/56)BIOMD0000000030.xml
Markevich2005_MAPK_AllRandomElementary
PMID:14744999
41 (22/4/15)BIOMD0000000031.xml
Markevich2004_MAPK_orderedMM2kinases
PMID:14744999
307 (123/47/137)BIOMD0000000032.xml
Kofahl2004_pheromone
PMID:15300679
217 (113/26/78)BIOMD0000000033.xml
Brown2004_NGF_EGF_signaling
PMID:14525003
126 (65/28/33)BIOMD0000000034.xml
Smolen2004_CircClock
PMID:15111397
92 (37/16/39)BIOMD0000000035.xml
Vilar2002_Oscillator
PMID:11972055
33 (19/5/9)BIOMD0000000036.xml
Tyson1999_CircClock
PMID:10545344
73 (35/12/26)BIOMD0000000037.xml
Marwan_Genetics_2003
PMID:12750324
93 (55/10/28)BIOMD0000000038.xml
Rohwer2000_Phosphotransferase_System
PMID:10889194
49 (24/7/18)BIOMD0000000039.xml
Marhl_CaOscillations
PMID:11004387
34 (17/5/12)BIOMD0000000040.xml
Field1974_Oregonator
DOI:10.1063/1.1681288
80 (47/9/24)BIOMD0000000041.xml
Kongas2001_creatine
http://www.icsb-2001.org/...
130 (56/25/49)BIOMD0000000042.xml
Nielsen1998_Glycolysis
DOI:10.1016/S0301
-4622(98)00122-7
47 (26/7/14)BIOMD0000000043.xml
Borghans1997_CaOscillation_model1
DOI:10.1016/S0301
-4622(97)00010-0
60 (34/8/18)BIOMD0000000044.xml
Borghans1997_CaOscillation_model2
DOI:10.1016/S0301
-4622(97)00010-0
51 (27/8/16)BIOMD0000000045.xml
Borghans1997_CaOscillation_model3
DOI:10.1016/S0301
-4622(97)00010-0
105 (48/15/42)BIOMD0000000046.xml
Olsen2003_peroxidase
PMID:12823550
34 (23/4/7)BIOMD0000000047.xml
Oxhamre2005_Ca_oscillation
PMID:15596518
189 (97/25/67)BIOMD0000000048.xml
Kholodenko1999_EGFRsignaling
PMID:10514507
1018 (434/150/434)BIOMD0000000049.xml
Sasagawa2005_MAPK
PMID:15793571
102 (45/16/41)BIOMD0000000050.xml
Martins2003_AmadoriDegradation
PMID:12873422
73 (34/11/28)BIOMD0000000052.xml
Brands2002_MonosaccharideCasein
PMID:12405768
81 (44/12/25)BIOMD0000000053.xml
Ferreira2003_CML_generation2
PMID:12911334
29 (16/6/7)BIOMD0000000054.xml
Ataullahkhanov1996_Adenylate
PMID:8733433
-BIOMD0000000055.xml
Locke2005_CircClock
DOI:10.1038/msb4100018
-BIOMD0000000056.xml
Chen2004_CellCycle
PMID:15169868