-
1
-
-
79955570036
-
Minimum Information About a Simulation Experiment (MIASE)
-
Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin E, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller A, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro H, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N. Minimum Information About a Simulation Experiment (MIASE). PLoS Compututational Biology 2011, 7(4):e1001122.
-
(2011)
PLoS Compututational Biology
, vol.7
, Issue.4
-
-
Waltemath, D.1
Adams, R.2
Beard, D.A.3
Bergmann, F.T.4
Bhalla, U.S.5
Britten, R.6
Chelliah, V.7
Cooling, M.T.8
Cooper, J.9
Crampin, E.10
Garny, A.11
Hoops, S.12
Hucka, M.13
Hunter, P.14
Klipp, E.15
Laibe, C.16
Miller, A.17
Moraru, I.18
Nickerson, D.19
Nielsen, P.20
Nikolski, M.21
Sahle, S.22
Sauro, H.23
Schmidt, H.24
Snoep, J.L.25
Tolle, D.26
Wolkenhauer, O.27
Le Novère, N.28
more..
-
2
-
-
45749118607
-
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
-
10.1038/nbt.1411, 2771753, 18688244
-
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Clark AM, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology 2008, 26(8):889-896. 10.1038/nbt.1411, 2771753, 18688244.
-
(2008)
Nature Biotechnology
, vol.26
, Issue.8
, pp. 889-896
-
-
Taylor, C.F.1
Field, D.2
Sansone, S.A.3
Aerts, J.4
Apweiler, R.5
Ashburner, M.6
Ball, C.A.7
Binz, P.A.8
Bogue, M.9
Booth, T.10
Brazma, A.11
Brinkman, R.R.12
Clark, A.M.13
Deutsch, E.W.14
Fiehn, O.15
Fostel, J.16
Ghazal, P.17
Gibson, F.18
Gray, T.19
Grimes, G.20
Hancock, J.M.21
Hardy, N.W.22
Hermjakob, H.23
Julian, R.K.24
Kane, M.25
Kettner, C.26
Kinsinger, C.27
Kolker, E.28
Kuiper, M.29
Le Novère, N.30
more..
-
3
-
-
0037342537
-
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
-
10.1093/bioinformatics/btg015, 12611808
-
Hucka M, Finney A, Sauro H, Bolouri H, Doyle J, Kitano H, Arkin A, Bornstein B, Bray D, Cornish-Bowden A, Cuellar A, Dronov S, Gilles E, Ginkel M, Gor V, Goryanin I, Hedley W, Hodgman T, Hofmeyr JH, Hunter P, Juty N, Kasberger J, Kremling A, Kummer U, Le Novère N, Loew L, Lucio D, Mendes P, Minch E, Mjolsness E, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19(4):524-31. 10.1093/bioinformatics/btg015, 12611808.
-
(2003)
Bioinformatics
, vol.19
, Issue.4
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.3
Bolouri, H.4
Doyle, J.5
Kitano, H.6
Arkin, A.7
Bornstein, B.8
Bray, D.9
Cornish-Bowden, A.10
Cuellar, A.11
Dronov, S.12
Gilles, E.13
Ginkel, M.14
Gor, V.15
Goryanin, I.16
Hedley, W.17
Hodgman, T.18
Hofmeyr, J.H.19
Hunter, P.20
Juty, N.21
Kasberger, J.22
Kremling, A.23
Kummer, U.24
Le Novère, N.25
Loew, L.26
Lucio, D.27
Mendes, P.28
Minch, E.29
Mjolsness, E.30
more..
-
4
-
-
1342329447
-
An Overview of CellML 1.1, a Biological Model Description Language
-
Cuellar AA, Lloyd CM, Nielsen PF, Bullivant DP, Nickerson DP, Hunter PJ. An Overview of CellML 1.1, a Biological Model Description Language. SIMULATION 2003, 79(12):740-747.
-
(2003)
SIMULATION
, vol.79
, Issue.12
, pp. 740-747
-
-
Cuellar, A.A.1
Lloyd, C.M.2
Nielsen, P.F.3
Bullivant, D.P.4
Nickerson, D.P.5
Hunter, P.J.6
-
5
-
-
77955483472
-
NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail
-
2887454, 20585541
-
Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, Barnes SR, Dimitrova YD, Silver RA. NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Computational Biology 2010, 6(6):e1000815+. 2887454, 20585541.
-
(2010)
PLoS Computational Biology
, vol.6
, Issue.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
Barnes, S.R.11
Dimitrova, Y.D.12
Silver, R.A.13
-
6
-
-
40349100409
-
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
-
Laibe C, Le Novère N. MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. BMC Systems Biology 2007, 58.
-
(2007)
BMC Systems Biology
, vol.58
-
-
Laibe, C.1
Le Novère, N.2
-
7
-
-
84857792407
-
Mathematical Markup Language (MathML) version 2.0. W3C recommendation
-
Ausbrooks R, Buswell S, Carlisle D, Dalmas S, Devitt S, Diaz A, Froumentin M, Hunter R, Ion P, Kohlhase M, Miner R, Poppelier N, Smith B, Soiffer N, Sutor R, Watt S. Mathematical Markup Language (MathML) version 2.0. W3C recommendation. World Wide Web Consortium 2003,
-
(2003)
World Wide Web Consortium
-
-
Ausbrooks, R.1
Buswell, S.2
Carlisle, D.3
Dalmas, S.4
Devitt, S.5
Diaz, A.6
Froumentin, M.7
Hunter, R.8
Ion, P.9
Kohlhase, M.10
Miner, R.11
Poppelier, N.12
Smith, B.13
Soiffer, N.14
Sutor, R.15
Watt, S.16
-
9
-
-
80155212661
-
Controlled vocabularies and semantics in Systems Biology
-
Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell D, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Ro-driguez N, Villeger A, Wilkinson D, Wimalaratne S, Laibe C, Hucka M, Le Novère N. Controlled vocabularies and semantics in Systems Biology. Molecular Systems Biology 2011, 7(543).
-
(2011)
Molecular Systems Biology
, vol.7
, Issue.543
-
-
Courtot, M.1
Juty, N.2
Knüpfer, C.3
Waltemath, D.4
Zhukova, A.5
Dräger, A.6
Dumontier, M.7
Finney, A.8
Golebiewski, M.9
Hastings, J.10
Hoops, S.11
Keating, S.12
Kell, D.13
Kerrien, S.14
Lawson, J.15
Lister, A.16
Lu, J.17
Machne, R.18
Mendes, P.19
Pocock, M.20
Ro-driguez, N.21
Villeger, A.22
Wilkinson, D.23
Wimalaratne, S.24
Laibe, C.25
Hucka, M.26
Le Novère, N.27
more..
-
10
-
-
0033532569
-
Chaos and birhythmicity in a model for circadian oscillations of the PER and TIM proteins in Drosophila
-
10.1006/jtbi.1999.0924, 10366496
-
Leloup J, Goldbeter A. Chaos and birhythmicity in a model for circadian oscillations of the PER and TIM proteins in Drosophila. Journal of theoretical biology 1999, 198(3):445-459. 10.1006/jtbi.1999.0924, 10366496.
-
(1999)
Journal of theoretical biology
, vol.198
, Issue.3
, pp. 445-459
-
-
Leloup, J.1
Goldbeter, A.2
-
11
-
-
77951953604
-
SBRML: a markup language for associating systems biology data with models
-
Dada JO, Spasić I, Paton NW, Mendes P. SBRML: a markup language for associating systems biology data with models. Bioinformatics (Oxford, England) 2010, 26(7):932-938.
-
(2010)
Bioinformatics (Oxford, England)
, vol.26
, Issue.7
, pp. 932-938
-
-
Dada, J.O.1
Spasić, I.2
Paton, N.W.3
Mendes, P.4
-
12
-
-
77954274688
-
BioCatalogue: a universal catalogue of web services for the life sciences
-
2896129, 20484378
-
Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble C. BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic acids research 2010, 38(suppl 2):W689. 2896129, 20484378.
-
(2010)
Nucleic acids research
, vol.38
, Issue.SUPPL. 2
-
-
Bhagat, J.1
Tanoh, F.2
Nzuobontane, E.3
Laurent, T.4
Orlowski, J.5
Roos, M.6
Wolstencroft, K.7
Aleksejevs, S.8
Stevens, R.9
Pettifer, S.10
Lopez, R.11
Goble, C.12
-
13
-
-
67149131701
-
CellML metadata standards, associated tools and repositories
-
10.1098/rsta.2008.0310, 3268215, 19380315
-
Beard DA, Britten R, Cooling MT, Garny A, Halstead MD, Hunter PJ, Lawson J, Lloyd CM, Marsh J, Miller A, Nickerson DP, Nielsen PM, Nomura T, Subramanium S, Wimalaratne SM, Yu T. CellML metadata standards, associated tools and repositories. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 2009, 367(1895):1845-1867. 10.1098/rsta.2008.0310, 3268215, 19380315.
-
(2009)
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences
, vol.367
, Issue.1895
, pp. 1845-1867
-
-
Beard, D.A.1
Britten, R.2
Cooling, M.T.3
Garny, A.4
Halstead, M.D.5
Hunter, P.J.6
Lawson, J.7
Lloyd, C.M.8
Marsh, J.9
Miller, A.10
Nickerson, D.P.11
Nielsen, P.M.12
Nomura, T.13
Subramanium, S.14
Wimalaratne, S.M.15
Yu, T.16
-
14
-
-
65149101663
-
Version control of pathway models using XML patches
-
Saffrey P, Orton R. Version control of pathway models using XML patches. BMC Sytems Biology 2009, 3:34.
-
(2009)
BMC Sytems Biology
, vol.3
, pp. 34
-
-
Saffrey, P.1
Orton, R.2
-
17
-
-
70350669878
-
IBioSim: a tool for the analysis and design of genetic circuits
-
10.1093/bioinformatics/btp457, 19628507
-
Myers C, Barker N, Jones K, Kuwahara H, Madsen C, Nguyen N. iBioSim: a tool for the analysis and design of genetic circuits. Bioinformatics 2009, 25(21):2848. 10.1093/bioinformatics/btp457, 19628507.
-
(2009)
Bioinformatics
, vol.25
, Issue.21
, pp. 2848
-
-
Myers, C.1
Barker, N.2
Jones, K.3
Kuwahara, H.4
Madsen, C.5
Nguyen, N.6
-
18
-
-
33845368513
-
COPASI - a COmplex PAthway SImulator
-
10.1093/bioinformatics/btl485, 17032683
-
Hoops S, Sahle S, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U. COPASI - a COmplex PAthway SImulator. Bioinformatics 2006, 22(24):3067-3074. 10.1093/bioinformatics/btl485, 17032683.
-
(2006)
Bioinformatics
, vol.22
, Issue.24
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Lee, C.3
Pahle, J.4
Simus, N.5
Singhal, M.6
Xu, L.7
Mendes, P.8
Kummer, U.9
-
19
-
-
40749162829
-
LibSBML: an API Library for SBML
-
10.1093/bioinformatics/btn051, 2517632, 18252737
-
Bornstein BJ, Keating SM, Jouraku A, Hucka M. LibSBML: an API Library for SBML. Bioinformatics 2008, 24(6):880-881. 10.1093/bioinformatics/btn051, 2517632, 18252737.
-
(2008)
Bioinformatics
, vol.24
, Issue.6
, pp. 880-881
-
-
Bornstein, B.J.1
Keating, S.M.2
Jouraku, A.3
Hucka, M.4
-
20
-
-
84874661973
-
An overview of the CellML API and its implementation
-
10.1186/1471-2105-11-178, 2858041, 20377909
-
Miller A, Marsh J, Reeve A, Garny A, Britten R, Halstead M, Cooper J, Nickerson D, Nielsen P. An overview of the CellML API and its implementation. BMC bioinformatics 2010, 11:178. 10.1186/1471-2105-11-178, 2858041, 20377909.
-
(2010)
BMC bioinformatics
, vol.11
, pp. 178
-
-
Miller, A.1
Marsh, J.2
Reeve, A.3
Garny, A.4
Britten, R.5
Halstead, M.6
Cooper, J.7
Nickerson, D.8
Nielsen, P.9
-
21
-
-
33644877164
-
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
-
1347454, 16381960
-
Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research 2006, 34(suppl 1):D689-D691. 1347454, 16381960.
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.SUPPL. 1
-
-
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
Snoep, J.L.11
Hucka, M.12
-
22
-
-
4544344218
-
Web-based kinetic modelling using JWS Online
-
10.1093/bioinformatics/bth200, 15072998
-
Olivier B, Snoep J. Web-based kinetic modelling using JWS Online. Bioinformatics 2004, 20(13):2143. 10.1093/bioinformatics/bth200, 15072998.
-
(2004)
Bioinformatics
, vol.20
, Issue.13
, pp. 2143
-
-
Olivier, B.1
Snoep, J.2
-
23
-
-
77956333400
-
Systematic integration of experimental data and models in systems biology
-
3008707, 21114840
-
Li P, Dada J, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW. Systematic integration of experimental data and models in systems biology. BMC bioinformatics 2010, 11:582. 3008707, 21114840.
-
(2010)
BMC bioinformatics
, vol.11
, pp. 582
-
-
Li, P.1
Dada, J.2
Jameson, D.3
Spasic, I.4
Swainston, N.5
Carroll, K.6
Dunn, W.7
Khan, F.8
Malys, N.9
Messiha, H.L.10
Simeonidis, E.11
Weichart, D.12
Winder, C.13
Wishart, J.14
Broomhead, D.S.15
Goble, C.A.16
Gaskell, S.J.17
Kell, D.B.18
Westerhoff, H.V.19
Mendes, P.20
Paton, N.W.21
more..
-
25
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
10.1038/35002125, 10659856
-
Elowitz M, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403(6767):335-338. 10.1038/35002125, 10659856.
-
(2000)
Nature
, vol.403
, Issue.6767
, pp. 335-338
-
-
Elowitz, M.1
Leibler, S.2
|