(en) A. Finney et M. Hucka, « Systems biology markup language: Level 2 and beyond », Biochemical Society Transactions, vol. 31, no 6, , p. 1472-1473 (PMID14641091, DOI10.1042/BST0311472, lire en ligne [PDF], consulté le ).
caltech.edu
authors.library.caltech.edu
(en) Andrew Finney, Michael Hucka, Benjamin J. Bornstein, Sarah M. Keating, Bruce E. Shapiro, Joanne Matthews, Ben L. Kovitz, Maria J. Schilstra, Akira Funahashi, John Doyle et Hiroaki Kitano, « Software Infrastructure for Effective Communication and Reuse of Computational Models », dans Zoltan Szallasi, Jorg Stelling et Vipul Periwal, System Modeling in Cellular Biology : From Concepts to Nuts and Bolts, Cambridge, MIT Press, , 448 p. (ISBN9780262195485, DOI10.7551/mitpress/9780262195485.003.0017, lire en ligne).
doi.org
dx.doi.org
(en) M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle, H. Kitano, A. P. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden et al., « The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models », Bioinformatics, vol. 19, no 4, , p. 524-531 (PMID12611808, DOI10.1093/bioinformatics/btg015, lire en ligne [PDF], consulté le ).
(en) A. Finney et M. Hucka, « Systems biology markup language: Level 2 and beyond », Biochemical Society Transactions, vol. 31, no 6, , p. 1472-1473 (PMID14641091, DOI10.1042/BST0311472, lire en ligne [PDF], consulté le ).
(en) M. Hucka, A. Finney, B.J. Bornstein, S.M. Keating, B.E. Shapiro, J. Matthews, B.L. Kovitz, M.J. Schilstra, A. Funahashi, J.C. Doyle et H. Kitano, « Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project », Systems Biology, IEE Proceedings, vol. 1, no 1, , p. 41-53 (ISSN1741-2471, PMID17052114, DOI10.1049/sb:20045008).
(en) Douglas B. Kella et Pedro Mendes, « The markup is the model : Reasoning about systems biology models in the Semantic Web era », Journal of Theoretical Biology, vol. 252, no 3, , p. 538-543 (PMID18054049, DOI10.1016/j.jtbi.2007.10.023).
(en) Andrew Finney, Michael Hucka, Benjamin J. Bornstein, Sarah M. Keating, Bruce E. Shapiro, Joanne Matthews, Ben L. Kovitz, Maria J. Schilstra, Akira Funahashi, John Doyle et Hiroaki Kitano, « Software Infrastructure for Effective Communication and Reuse of Computational Models », dans Zoltan Szallasi, Jorg Stelling et Vipul Periwal, System Modeling in Cellular Biology : From Concepts to Nuts and Bolts, Cambridge, MIT Press, , 448 p. (ISBN9780262195485, DOI10.7551/mitpress/9780262195485.003.0017, lire en ligne).
Jeffrey D Orth, Ines Thiele et Bernhard O Palsson, « What is flux balance analysis? », Nature Biotechnology, vol. 28, no 3, , p. 245–248 (PMID20212490, PMCID3108565, DOI10.1038/nbt.1614).
Matthew A Oberhardt, Bernhard O Palsson et Jason A Papin, « Applications of genome-scale metabolic reconstructions », Molecular Systems Biology, vol. 5, no 1, , article no 320 (DOI10.1038/msb.2009.77)
Gregory Batt, Delphine Ropers, Hidde de Jong, Johannes Geiselmann, Radu Mateescu, Michel Page et Dominique Schneider, « Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli », Bioinformatics, vol. 21, , i19–i28 (PMID15961457, DOI10.1093/bioinformatics/bti1048).
Tomas Helikar, John Konvalina, Jack Heidel et Jim A Rogers, « Emergent decision-making in biological signal transduction networks », Proceedings of the National Academy of Sciences, vol. 105, no 6, , p. 1913 (DOI10.1073/pnas.0705088105).
Ralph Gauges, Ursula Rost, Sven Sahle et Katja Wegner, « A model diagram layout extension for SBML », Bioinformatics, vol. 22, no 15, , p. 1879–85 (PMID16709586, DOI10.1093/bioinformatics/btl195).
(en) M. Hucka, A. Finney, B.J. Bornstein, S.M. Keating, B.E. Shapiro, J. Matthews, B.L. Kovitz, M.J. Schilstra, A. Funahashi, J.C. Doyle et H. Kitano, « Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project », Systems Biology, IEE Proceedings, vol. 1, no 1, , p. 41-53 (ISSN1741-2471, PMID17052114, DOI10.1049/sb:20045008).
nih.gov
ncbi.nlm.nih.gov
(en) M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle, H. Kitano, A. P. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden et al., « The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models », Bioinformatics, vol. 19, no 4, , p. 524-531 (PMID12611808, DOI10.1093/bioinformatics/btg015, lire en ligne [PDF], consulté le ).
(en) A. Finney et M. Hucka, « Systems biology markup language: Level 2 and beyond », Biochemical Society Transactions, vol. 31, no 6, , p. 1472-1473 (PMID14641091, DOI10.1042/BST0311472, lire en ligne [PDF], consulté le ).
(en) M. Hucka, A. Finney, B.J. Bornstein, S.M. Keating, B.E. Shapiro, J. Matthews, B.L. Kovitz, M.J. Schilstra, A. Funahashi, J.C. Doyle et H. Kitano, « Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project », Systems Biology, IEE Proceedings, vol. 1, no 1, , p. 41-53 (ISSN1741-2471, PMID17052114, DOI10.1049/sb:20045008).
(en) Douglas B. Kella et Pedro Mendes, « The markup is the model : Reasoning about systems biology models in the Semantic Web era », Journal of Theoretical Biology, vol. 252, no 3, , p. 538-543 (PMID18054049, DOI10.1016/j.jtbi.2007.10.023).
Jeffrey D Orth, Ines Thiele et Bernhard O Palsson, « What is flux balance analysis? », Nature Biotechnology, vol. 28, no 3, , p. 245–248 (PMID20212490, PMCID3108565, DOI10.1038/nbt.1614).
Gregory Batt, Delphine Ropers, Hidde de Jong, Johannes Geiselmann, Radu Mateescu, Michel Page et Dominique Schneider, « Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli », Bioinformatics, vol. 21, , i19–i28 (PMID15961457, DOI10.1093/bioinformatics/bti1048).
Ralph Gauges, Ursula Rost, Sven Sahle et Katja Wegner, « A model diagram layout extension for SBML », Bioinformatics, vol. 22, no 15, , p. 1879–85 (PMID16709586, DOI10.1093/bioinformatics/btl195).
(en) M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle, H. Kitano, A. P. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden et al., « The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models », Bioinformatics, vol. 19, no 4, , p. 524-531 (PMID12611808, DOI10.1093/bioinformatics/btg015, lire en ligne [PDF], consulté le ).