-
1
-
-
0037342537
-
The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models
-
PubMed doi:10.1093/bioinformatics/btg015
-
Hucka M, Bolouri H, Finney A, Sauro HM, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, et al. The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 2003; 19:524-531. PubMed doi:10.1093/bioinformatics/btg015
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
Bolouri, H.2
Finney, A.3
Sauro, H.M.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
-
2
-
-
77956664073
-
BioPAX-A community standard for pathway data sharing
-
PubMed doi:10.1038/nbt.1666
-
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J. BioPAX-A community standard for pathway data sharing. Nat Biotechnol 2010; 28:935-942. PubMed doi:10.1038/nbt.1666
-
(2010)
Nat Biotechnol
, vol.28
, pp. 935-942
-
-
Demir, E.1
Cary, M.P.2
Paley, S.3
Fukuda, K.4
Lemer, C.5
Vastrik, I.6
Wu, G.7
D'Eustachio, P.8
Schaefer, C.9
Luciano, J.10
-
3
-
-
68449103579
-
The Systems Biology Graphical Notation
-
PubMed doi:10.1038/nbt.1558
-
Le Novère N, Hucka M, Mi H, Moodie S, Shreiber F, Sorokin A, Demir E, Wegner K, Aladjem M, Wimalaratne S, et al. The Systems Biology Graphical Notation. Nat Biotechnol 2009; 27:735-741. PubMed doi:10.1038/nbt.1558
-
(2009)
Nat Biotechnol
, vol.27
, pp. 735-741
-
-
le Novère, N.1
Hucka, M.2
Mi, H.3
Moodie, S.4
Shreiber, F.5
Sorokin, A.6
Demir, E.7
Wegner, K.8
Aladjem, M.9
Wimalaratne, S.10
-
4
-
-
67650671892
-
Adding semantics in kinetics models of biochemical pathways
-
Available at
-
Le Novère N, Courtot M, Laibe C. Adding semantics in kinetics models of biochemical pathways. Proc 2nd Intl Symp Exp Std Cond Enz Charact 2007; 137-53. Available at http:// www.beilstein-institut.de/index.php?id=196
-
(2007)
Proc 2nd Intl Symp Exp Std Cond Enz Charact
, pp. 137-153
-
-
le Novère, N.1
Courtot, M.2
Laibe, C.3
-
5
-
-
2442595958
-
CellML, its future, present and past
-
PubMed doi:10.1016/j.pbiomolbio.2004.01.004
-
Lloyd CM, Halstead MD, Nielsen PF. CellML, its future, present and past. Prog Biophys Mol Biol 2004; 85:433-450. PubMed doi:10.1016/j.pbiomolbio.2004.01.004
-
(2004)
Prog Biophys Mol Biol
, vol.85
, pp. 433-450
-
-
Lloyd, C.M.1
Halstead, M.D.2
Nielsen, P.F.3
-
6
-
-
77955483472
-
NeuroML: A language for describing data driven models of neurons and networks with a high degree of biological detail
-
PubMed doi:10.1371/journal.pcbi.1000815
-
Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, et al. NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLOS Comput Biol 2010; 6:e1000815. PubMed doi:10.1371/journal.pcbi.1000815
-
(2010)
PLOS Comput Biol
, vol.6
-
-
Gleeson, P.1
Crook, S.2
Cannon, R.C.3
Hines, M.L.4
Billings, G.O.5
Farinella, M.6
Morse, T.M.7
Davison, A.P.8
Ray, S.9
Bhalla, U.S.10
-
7
-
-
57049184135
-
SED-ML-An XML Format for the implementation of the MIASE guidelines
-
Köhn D, Le Novère N. SED-ML-An XML Format for the implementation of the MIASE guidelines. Lect Notes Bioinfo 2008; 5307:176-190.
-
(2008)
Lect Notes Bioinfo
, vol.5307
, pp. 176-190
-
-
Köhn, D.1
le Novère, N.2
-
8
-
-
85177698067
-
-
COMBINE. http://co.mbine.org
-
COMBINE
-
-
-
9
-
-
71849095864
-
TinkerCell: Modular CAD tool for synthetic biology
-
PubMed doi:10.1186/1754-1611-3-19
-
Chandran D, Bergmann FT, Sauro HM. TinkerCell: modular CAD tool for synthetic biology. J Biol Eng 2009; 3:19. PubMed doi:10.1186/1754-1611-3-19
-
(2009)
J Biol Eng
, vol.3
, pp. 19
-
-
Chandran, D.1
Bergmann, F.T.2
Sauro, H.M.3
-
10
-
-
85177638729
-
-
Cell ML. http:// www.cellml.org
-
Cell ML
-
-
-
11
-
-
85177639977
-
-
Field ML. http://www.physiome.org.nz/xml_languages/fieldml
-
Field ML
-
-
-
15
-
-
85177650453
-
-
OpenCell. http://www.cellml.org/tools/opencell
-
OpenCell
-
-
-
18
-
-
85177664482
-
-
API library libSedML. http://libsedml.sourceforge.net/libSedML/Welcome.html
-
API library libSedML
-
-
-
21
-
-
85177682332
-
-
SBSI. http://www.sbsi.ed.ac.uk
-
SBSI
-
-
-
28
-
-
85177682905
-
-
Arcadia. http:// arcadiapathways.sourceforge.net
-
Arcadia
-
-
-
29
-
-
85177652631
-
-
VISIBIOweb. http:// www.bilkent.edu.tr/~bcbi/pvs.html
-
VISIBIOweb
-
-
-
38
-
-
85177686357
-
-
BioUML. http:// www.biouml.org
-
BioUML
-
-
-
42
-
-
85177645851
-
-
Commons P. http:// www.pathwaycommons.org
-
-
-
Commons, P.1
-
43
-
-
78651332286
-
Pathway Commons, a web resource for biological pathway data
-
PubMed doi:10.1093/nar/gkq1039
-
Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res 2011; 39:D685-D690. PubMed doi:10.1093/nar/gkq1039
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Cerami, E.G.1
Gross, B.E.2
Demir, E.3
Rodchenkov, I.4
Babur, O.5
Anwar, N.6
Schultz, N.7
Bader, G.D.8
Sander, C.9
-
44
-
-
85177666207
-
-
BioPAX. http:// www.biopax.org
-
BioPAX
-
-
-
52
-
-
77955385319
-
Ranked Retrieval of Computational Biology Models
-
PubMed
-
Henkel R, Endler L, Le Novère N, Peters A, Waltemath D. Ranked Retrieval of Computational Biology Models. BMC Bioinformatics 2010; 11:423. PubMed
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 423
-
-
Henkel, R.1
Endler, L.2
le Novère, N.3
Peters, A.4
Waltemath, D.5
-
53
-
-
85177666374
-
-
Semantic SBML. http://www.semanticsbml.org
-
Semantic SBML
-
-
-
55
-
-
79960596028
-
Retrieval, alignment, and clustering of computational models based on semantic annotations
-
PubMed doi:10.1038/msb.2011.41
-
Schulz M, Krause F, Le Novère N, Klipp E, Liebermeister W. Retrieval, alignment, and clustering of computational models based on semantic annotations. Mol Syst Biol 2011; 7:512. PubMed doi:10.1038/msb.2011.41
-
(2011)
Mol Syst Biol
, vol.7
, pp. 512
-
-
Schulz, M.1
Krause, F.2
le Novère, N.3
Klipp, E.4
Liebermeister, W.5
-
57
-
-
54249091564
-
Presenting and exploring biological pathways with PathVisio
-
PubMed doi:10.1186/1471-2105-9-399
-
van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, Evelo C. Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics 2008; 9:399. PubMed doi:10.1186/1471-2105-9-399
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 399
-
-
van Iersel, M.P.1
Kelder, T.2
Pico, A.R.3
Hanspers, K.4
Coort, S.5
Conklin, B.R.6
Evelo, C.7
-
58
-
-
84874650571
-
-
WikiPathways. http://www.wikipathways.org
-
WikiPathways
-
-
-
59
-
-
48349105261
-
WikiPathways: Pathway editing for the people
-
PubMed doi:10.1371/journal.pbio.0060184
-
Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol 2008; 6:e184. PubMed doi:10.1371/journal.pbio.0060184
-
(2008)
PLoS Biol
, vol.6
-
-
Pico, A.R.1
Kelder, T.2
van Iersel, M.P.3
Hanspers, K.4
Conklin, B.R.5
Evelo, C.6
-
64
-
-
77953934646
-
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
-
PubMed doi:10.1186/1752-0509-4-92
-
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, et al. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 2010; 4:92. PubMed doi:10.1186/1752-0509-4-92
-
(2010)
BMC Syst Biol
, vol.4
, pp. 92
-
-
Li, C.1
Donizelli, M.2
Rodriguez, N.3
Dharuri, H.4
Endler, L.5
Chelliah, V.6
Li, L.7
He, E.8
Henry, A.9
Stefan, M.I.10
-
66
-
-
0742323374
-
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data
-
PubMed doi:10.1038/nbt926
-
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, et al. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol 2004; 22:177-183. PubMed doi:10.1038/nbt926
-
(2004)
Nat Biotechnol
, vol.22
, pp. 177-183
-
-
Hermjakob, H.1
Montecchi-Palazzi, L.2
Bader, G.3
Wojcik, J.4
Salwinski, L.5
Ceol, A.6
Moore, S.7
Orchard, S.8
Sarkans, U.9
von Mering, C.10
-
67
-
-
30044440098
-
Molecular interaction maps of bioregulatory networks: A general rubric for systems biology
-
PubMed doi:10.1091/mbc.E05-09-0824
-
Kohn KW, Aladjem MI, Weinstein JN, Pommier Y. Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol Biol Cell 2005; 17:1-13. PubMed doi:10.1091/mbc.E05-09-0824
-
(2005)
Mol Biol Cell
, vol.17
, pp. 1-13
-
-
Kohn, K.W.1
Aladjem, M.I.2
Weinstein, J.N.3
Pommier, Y.4
-
69
-
-
85177689596
-
-
BiNoM. http://bioinfo-out.curie.fr/projects/binom
-
BiNoM
-
-
-
71
-
-
85177650428
-
-
Neuro ML. http://www.neuroml.org
-
Neuro ML
-
-
-
75
-
-
85177657445
-
-
SBML. http://sbml.org
-
SBML
-
-
-
76
-
-
85177656909
-
-
Available from Nat Preced doi:10.1038/npre.2010.5011.2
-
Hucka M. SBML Level 3 Brief Update. Available from Nat Preced 2010 doi:10.1038/npre.2010.5011.2
-
(2010)
SBML Level 3 Brief Update
-
-
Hucka, M.1
-
80
-
-
85177665134
-
-
ibSBML. http://sbml.org/Software/libSBML
-
ibSBML
-
-
-
84
-
-
70350669878
-
iBioSim: A tool for the analysis and design of genetic circuits
-
PubMed doi:10.1093/bioinformatics/btp457
-
Myers CJ, Barker N, Jones K, Kuwahara H, Madsen C, Nguyen NP. iBioSim: a tool for the analysis and design of genetic circuits. Bioinformatics 2009; 25:2848-2849. PubMed doi:10.1093/bioinformatics/btp457
-
(2009)
Bioinformatics
, vol.25
, pp. 2848-2849
-
-
Myers, C.J.1
Barker, N.2
Jones, K.3
Kuwahara, H.4
Madsen, C.5
Nguyen, N.P.6
-
85
-
-
85177683640
-
-
iBioSim. http://www.async.ece.utah.edu/iBioSim
-
iBioSim
-
-
-
86
-
-
85177685172
-
-
Available from Nat Preced doi:10.1038/npre.2010.4983.1
-
Dräger A, Nitschmann S, Dörr A, Eichner J, Ziller M, Zell A. Context-based generation of kinetic equations with SBMLsqueezer 1.3. Available from Nat Preced 2010 doi:10.1038/npre.2010.4983.1
-
(2010)
Context-based generation of kinetic equations with SBMLsqueezer 1.3
-
-
Dräger, A.1
Nitschmann, S.2
Dörr, A.3
Eichner, J.4
Ziller, M.5
Zell, A.6
-
87
-
-
85177640870
-
-
SBMLsqueezer. http:// www.ra.cs.uni-tuebingen.de/software/SBMLsqueezer
-
SBMLsqueezer
-
-
-
88
-
-
85177657982
-
-
Crdata. http:// crdata.org
-
Crdata
-
-
-
89
-
-
85177674962
-
-
SBOL. http:// www.sbolstandard.org
-
SBOL
-
-
-
91
-
-
85177635010
-
-
SBGN-PD. http:// www.sbgn.org/Discussion_on_Issues
-
SBGN-PD
-
-
-
92
-
-
85177649144
-
-
Activity flow. http:// www.sbgn.org/AF_node
-
Activity flow
-
-
-
94
-
-
85177673923
-
-
KEGG pathways to SBML. http:// www.ra.cs.uni-tuebingen.de/software/KEGGtranslator
-
KEGG pathways to SBML
-
-
-
95
-
-
85177647263
-
-
Kinetic SAO. http:// www.biomodels.net/kisao
-
Kinetic SAO
-
-
|