-
1
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A et al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics, 19, 524-531.
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
-
2
-
-
2442595958
-
CellML: Its future, present and past
-
Lloyd, C. M., Halstead, M. D. and Nielsen, P. F. (2004) CellML: its future, present and past. Progr. Biophys. Mol. Biol., 85, 433-450.
-
(2004)
Progr. Biophys. Mol. Biol.
, vol.85
, pp. 433-450
-
-
Lloyd, C.M.1
Halstead, M.D.2
Nielsen, P.F.3
-
3
-
-
33644877164
-
BioModels Database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
-
Le Novère, N., Bornstein, B., Broicher, A., Courtot, M., Donizelli, M., Dharuri, H., Li, L., Sauro, H., Schilstra, M., Shapiro, B. et al. (2006) BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res., 34, D689-D691.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. D689-D691
-
-
Le Novère, N.1
Bornstein, B.2
Broicher, A.3
Courtot, M.4
Donizelli, M.5
Dharuri, H.6
Li, L.7
Sauro, H.8
Schilstra, M.9
Shapiro, B.10
-
4
-
-
77953934646
-
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
-
Li, C., Donizelli, M., Rodriguez, N., Dharuri, H., Endler, L., Chelliah, V., Li, L., He, E., Henry, A., Stefan, M. I. et al. (2010) BioModels Database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst. Biol., 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
-
5
-
-
84891783174
-
Activities at the Universal Protein Resource (UniProt)
-
The UniProt Consortium. (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res., 42, D191-198.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D191-D198
-
-
The UniProt Consortium1
-
6
-
-
84862156032
-
Identifiers.org and MIRIAM Registry: Community resources to provide persistent identification
-
Juty, N., Le Novère, N. and Laibe, C. (2012) Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res., 40, D580-D586.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D580-D586
-
-
Juty, N.1
Le Novère, N.2
Laibe, C.3
-
7
-
-
28644433993
-
Minimum information requested in the annotation of biochemical models (MIRIAM)
-
Le Novère, N., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P. et al. (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol., 23, 1509-1515.
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 1509-1515
-
-
Le Novère, N.1
Finney, A.2
Hucka, M.3
Bhalla, U.S.4
Campagne, F.5
Collado-Vides, J.6
Crampin, E.J.7
Halstead, M.8
Klipp, E.9
Mendes, P.10
-
8
-
-
84886740491
-
Path2Models: Large-scale generation of computational models from biochemical pathway maps
-
Büchel, F., Rodriguez, N., Swainston, N., Wrzodek, C., Czauderna, T., Keller, R., Mittag, F., Schubert, M., Glont, M., Golebiewski, M. et al. (2013) Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol., 7, 116.
-
(2013)
BMC Syst. Biol.
, vol.7
, pp. 116
-
-
Büchel, F.1
Rodriguez, N.2
Swainston, N.3
Wrzodek, C.4
Czauderna, T.5
Keller, R.6
Mittag, F.7
Schubert, M.8
Glont, M.9
Golebiewski, M.10
-
9
-
-
84891760956
-
Data, information, knowledge and principle: Back to metabolism in KEGG
-
Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res., 42, D199-D205.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D199-D205
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Kawashima, M.4
Furumichi, M.5
Tanabe, M.6
-
10
-
-
84891774001
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
-
Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C. A., Holland, T. A., Keseler, I. M., Kothari, A., Kubo, A. et al. (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res., 42, D459-D471.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D459-D471
-
-
Caspi, R.1
Altman, T.2
Billington, R.3
Dreher, K.4
Foerster, H.5
Fulcher, C.A.6
Holland, T.A.7
Keseler, I.M.8
Kothari, A.9
Kubo, A.10
-
11
-
-
84862214722
-
SABIO-RK-database for biochemical reaction kinetics
-
Wittig, U., Kania, R., Golebiewski, M., Rey, M., Shi, L., Jong, L., Algaa, E., Weidemann, A., Sauer-Danzwith, H., Mir, S. et al. (2012) SABIO-RK-database for biochemical reaction kinetics. Nucleic Acids Res., 40, D790-D796.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D790-D796
-
-
Wittig, U.1
Kania, R.2
Golebiewski, M.3
Rey, M.4
Shi, L.5
Jong, L.6
Algaa, E.7
Weidemann, A.8
Sauer-Danzwith, H.9
Mir, S.10
-
12
-
-
84870474617
-
Qualitative translation of relations from BioPAX to SBML qual
-
Büchel, F., Wrzodek, C., Mittag, F., Dräger, A., Eichner, J., Rodriguez, N., Le Novère, N. and Zell, A. (2012) Qualitative translation of relations from BioPAX to SBML qual. Bioinformatics, 28, 2648-2653.
-
(2012)
Bioinformatics
, vol.28
, pp. 2648-2653
-
-
Büchel, F.1
Wrzodek, C.2
Mittag, F.3
Dräger, A.4
Eichner, J.5
Rodriguez, N.6
Le Novère, N.7
Zell, A.8
-
13
-
-
58149186477
-
PID: The pathway interaction database
-
Schaefer, C. F., Anthony, K., Krupa, S., Buchoff, J., Day, M., Hannay, T. and Buetow, K. H. (2009) PID: the Pathway Interaction Database. Nucleic Acids Res., 37, D674-D679.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D674-D679
-
-
Schaefer, C.F.1
Anthony, K.2
Krupa, S.3
Buchoff, J.4
Day, M.5
Hannay, T.6
Buetow, K.H.7
-
14
-
-
84865123095
-
Software support for SBGN maps: SBGN-ML and LibSBGN
-
van Iersel, M. P., Villeger, A. C., Czauderna, T., Boyd, S. E., Bergmann, F. T., Luna, A., Demir, E., Sorokin, A., Dogrusoz, U., Matsuoka, Y. et al. (2012) Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics, 28, 2016-2021.
-
(2012)
Bioinformatics
, vol.28
, pp. 2016-2021
-
-
Van Iersel, M.P.1
Villeger, A.C.2
Czauderna, T.3
Boyd, S.E.4
Bergmann, F.T.5
Luna, A.6
Demir, E.7
Sorokin, A.8
Dogrusoz, U.9
Matsuoka, Y.10
-
15
-
-
77953888300
-
BioModels.net Web Services, a free and integrated toolkit for computational modelling software
-
Li, C., Courtot, M., Novère, N. and Laibe, C. (2010) BioModels.net Web Services, a free and integrated toolkit for computational modelling software. Briefings Bioinform., 11, 270-277.
-
(2010)
Briefings Bioinform.
, vol.11
, pp. 270-277
-
-
Li, C.1
Courtot, M.2
Novère, N.3
Laibe, C.4
-
16
-
-
84874253819
-
Gene Ontology annotations and resources
-
Gene Ontology Consortium, Blake, J. A., Dolan, M., Drabkin, H., Hill, D. P., Li, N., Sitnikov, D., Bridges, S., Burgess, S., Buza, T. et al. (2013) Gene Ontology annotations and resources. Nucleic Acids Res., 41, D530-D535.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D530-D535
-
-
Gene Ontology Consortium1
Blake, J.A.2
Dolan, M.3
Drabkin, H.4
Hill, D.P.5
Li, N.6
Sitnikov, D.7
Bridges, S.8
Burgess, S.9
Buza, T.10
-
17
-
-
65649112429
-
SBML2L (A) T (E) X: Conversion of SBML files into human-readable reports
-
Dräger, A., Planatscher, H., Motsou Wouamba, D., Schroder, A., Hucka, M., Endler, L., Golebiewski, M., Muller, W. and Zell, A. (2009) SBML2L (A) T (E) X: conversion of SBML files into human-readable reports. Bioinformatics, 25, 1455-1456.
-
(2009)
Bioinformatics
, vol.25
, pp. 1455-1456
-
-
Dräger, A.1
Planatscher, H.2
Motsou Wouamba, D.3
Schroder, A.4
Hucka, M.5
Endler, L.6
Golebiewski, M.7
Muller, W.8
Zell, A.9
-
19
-
-
84859339035
-
Spatial modeling of cell signaling networks
-
Cowan, A. E., Morar, I. I., Schaf, J. C., Slepchenko, B. M. and Loew, L. M. (2012) Spatial modeling of cell signaling networks. Methods in cell biology., 110 195-221.
-
(2012)
Methods in Cell biology.
, vol.110
, pp. 195-221
-
-
Cowan, A.E.1
Morar, I.I.2
Schaf, J.C.3
Slepchenko, B.M.4
Loew, L.M.5
-
20
-
-
4544344218
-
Web-based kinetic modelling using JWS Online
-
Oliver, B. G. and Snoep, J. L. (2004) Web-based kinetic modelling using JWS Online. Bioinformatics., 20, 2143-2144.
-
(2004)
Bioinformatics.
, vol.20
, pp. 2143-2144
-
-
Oliver, B.G.1
Snoep, J.L.2
-
21
-
-
84908689680
-
BioModels linked dataset
-
Wimalaratne, S. M., Grenon, P., Hermjakob, H., Le Novère, N. and Laibe, C. (2014) BioModels linked dataset. BMC Syst. Biol., 8, 91.
-
(2014)
BMC Syst. Biol.
, vol.8
, pp. 91
-
-
Wimalaratne, S.M.1
Grenon, P.2
Hermjakob, H.3
Le Novère, N.4
Laibe, C.5
-
22
-
-
84899523552
-
The EBI RDF platform: Linked open data for the life sciences
-
Jupp, S., Malone, J., Bolleman, J., Brandizi, M., Davies, M., Garcia, L., Gaulton, A., Gehant, S., Laibe, C., Redaschi, N. et al. (2014) The EBI RDF platform: linked open data for the life sciences. Bioinformatics, 30, 1338-1339.
-
(2014)
Bioinformatics
, vol.30
, pp. 1338-1339
-
-
Jupp, S.1
Malone, J.2
Bolleman, J.3
Brandizi, M.4
Davies, M.5
Garcia, L.6
Gaulton, A.7
Gehant, S.8
Laibe, C.9
Redaschi, N.10
-
23
-
-
84881162079
-
The impact of mathematical modeling on the understanding of diabetes and related complications
-
Ajmera, I., Swat, M., Laibe, C., Le Novère, N. and Chelliah, V. (2013) The impact of mathematical modeling on the understanding of diabetes and related complications. CPT: Pharmacom. Syst. Pharmacol., 2, e54.
-
(2013)
CPT: Pharmacom. Syst. Pharmacol.
, vol.2
, pp. e54
-
-
Ajmera, I.1
Swat, M.2
Laibe, C.3
Le Novère, N.4
Chelliah, V.5
-
24
-
-
84902159136
-
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology
-
Galdzicki, M., Clancy, K. P., Oberortner, E., Pocock, M., Quinn, J. Y., Rodriguez, C. A., Roehner, N., Wilson, M. L., Adam, L., Anderson, J. C. et al. (2014) The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nat. Biotechnol., 32, 545-550.
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 545-550
-
-
Galdzicki, M.1
Clancy, K.P.2
Oberortner, E.3
Pocock, M.4
Quinn, J.Y.5
Rodriguez, C.A.6
Roehner, N.7
Wilson, M.L.8
Adam, L.9
Anderson, J.C.10
-
25
-
-
77955483472
-
NeuroML: A language for describing data driven models of neurons and networks with a high degree of biological detail
-
Gleeson, P., Crook, S., Cannon, R. C., Hines, M. L., Billings, G. O., Farinella, M., Morse, T. M., Davison, A. P., Ray, S., Bhalla, U. S. et al. (2010) NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Comput. Biol., 6, e1000815.
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. e1000815
-
-
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
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