{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T16:48:16Z","timestamp":1761929296096},"reference-count":17,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2006,6,1]],"date-time":"2006-06-01T00:00:00Z","timestamp":1149120000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Nat Biotechnol"],"published-print":{"date-parts":[[2006,6]]},"DOI":"10.1038\/nbt0606-667","type":"journal-article","created":{"date-parts":[[2006,6,9]],"date-time":"2006-06-09T04:20:08Z","timestamp":1149826808000},"page":"667-672","source":"Crossref","is-referenced-by-count":146,"title":["Tools for kinetic modeling of biochemical networks"],"prefix":"10.1038","volume":"24","author":[{"given":"Rui","family":"Alves","sequence":"first","affiliation":[]},{"given":"Fernando","family":"Antunes","sequence":"additional","affiliation":[]},{"given":"Armindo","family":"Salvador","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"key":"BFnbt0606667_CR1","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","volume":"19","author":"M Hucka","year":"2003","unstructured":"Hucka, M. et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524\u2013531 (2003).","journal-title":"Bioinformatics"},{"key":"BFnbt0606667_CR2","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1177\/0037549703040939","volume":"79","author":"AA Cuellar","year":"2003","unstructured":"Cuellar, A.A. et al. An overview of CellML 1.1, a biological model description language. Simulation-Trans. Soc. Modeling Simul. Int. 79, 740\u2013747 (2003).","journal-title":"Simulation-Trans. Soc. Modeling Simul. Int."},{"key":"BFnbt0606667_CR3","doi-asserted-by":"publisher","first-page":"D689","DOI":"10.1093\/nar\/gkj092","volume":"34","author":"N Le Novere","year":"2006","unstructured":"Le Novere, N. et al. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34, D689\u2013D691 (2006).","journal-title":"Nucleic Acids Res."},{"key":"BFnbt0606667_CR4","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1089\/153623103322637670","volume":"7","author":"HM Sauro","year":"2003","unstructured":"Sauro, H.M. et al. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. OMICS 7, 355\u2013372 (2003).","journal-title":"OMICS"},{"key":"BFnbt0606667_CR5","doi-asserted-by":"publisher","first-page":"2923","DOI":"10.1093\/bioinformatics\/bti431","volume":"21","author":"J Hattne","year":"2005","unstructured":"Hattne, J., Fange, D. & Elf, J. Stochastic reaction-diffusion simulation with MesoRD. Bioinformatics 21, 2923\u20132924 (2005).","journal-title":"Bioinformatics"},{"key":"BFnbt0606667_CR6","doi-asserted-by":"publisher","DOI":"10.1007\/b98868","volume-title":"Mathematical Biology: An Introduction","author":"JD Murray","year":"2004","unstructured":"Murray, J.D. Mathematical Biology: An Introduction (Springer, New York, 2004)."},{"key":"BFnbt0606667_CR7","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1038\/229542a0","volume":"229","author":"MA Savageau","year":"1971","unstructured":"Savageau, M.A. Parameter sensitivity as a criterion for evaluating and comparing the performance of biochemical systems. Nature 229, 542\u2013544 (1971).","journal-title":"Nature"},{"key":"BFnbt0606667_CR8","doi-asserted-by":"publisher","first-page":"34909","DOI":"10.1074\/jbc.M002461200","volume":"275","author":"JM Rohwer","year":"2000","unstructured":"Rohwer, J.M., Meadow, N.D., Roseman, S., Westerhoff, H.V. & Postma, P.W. Understanding glucose transport by the bacterial phosphoenolpyruvate:glycose phosphotransferase system on the basis of kinetic measurements in vitro. J. Biol. Chem. 275, 34909\u201334921 (2000).","journal-title":"J. Biol. Chem."},{"key":"BFnbt0606667_CR9","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1016\/S1478-5382(03)02370-9","volume":"1","author":"A Funahashi","year":"2003","unstructured":"Funahashi, A., Tanimura, N., Morohashi, M. & Kitano, H. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. Biosilico 1, 156\u2013162 (2003).","journal-title":"Biosilico"},{"key":"BFnbt0606667_CR10","doi-asserted-by":"publisher","first-page":"1319","DOI":"10.1093\/bioinformatics\/bth067","volume":"20","author":"P Dhar","year":"2004","unstructured":"Dhar, P. et al. Cellware\u2013a multi-algorithmic software for computational systems biology. Bioinformatics 20, 1319\u20131321 (2004).","journal-title":"Bioinformatics"},{"key":"BFnbt0606667_CR11","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1142\/S0219720005001132","volume":"3","author":"S Ramsey","year":"2005","unstructured":"Ramsey, S., Orrell, D. & Bolouri, H. Dizzy: stochastic simulation of large-scale genetic regulatory networks. J. Bioinform. Comput. Biol. 3, 415\u2013436 (2005).","journal-title":"J. Bioinform. Comput. Biol."},{"key":"BFnbt0606667_CR12","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1093\/bioinformatics\/btg009","volume":"19","author":"L You","year":"2003","unstructured":"You, L., Hoonlor, A. & Yin, J. Modeling biological systems using Dynetica\u2013a simulator of dynamic networks. Bioinformatics 19, 435\u2013436 (2003).","journal-title":"Bioinformatics"},{"key":"BFnbt0606667_CR13","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1016\/S0968-0004(97)01103-1","volume":"22","author":"P Mendes","year":"1997","unstructured":"Mendes, P. Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22, 361\u2013363 (1997).","journal-title":"Trends Biochem. Sci."},{"key":"BFnbt0606667_CR14","volume-title":"Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists","author":"EO Voit","year":"2000","unstructured":"Voit, E.O. & Ferreira, A. Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists (Cambridge University Press, Cambridge, 2000)."},{"key":"BFnbt0606667_CR15","first-page":"386","volume":"18","author":"RB King","year":"1986","unstructured":"King, R.B., Budd, R., Bassingthwaighte, J.B. & Kootsey, J.M. A simulation system for biological investigators. Proc. Summer Comput. Simul. Conf. 18, 386\u2013389 (1986).","journal-title":"Proc. Summer Comput. Simul. Conf."},{"key":"BFnbt0606667_CR16","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1038\/nrm1051","volume":"4","author":"TB Kirkwood","year":"2003","unstructured":"Kirkwood, T.B. et al. Towards an e-biology of ageing: integrating theory and data. Nat. Rev. Mol. Cell Biol. 4, 243\u2013249 (2003).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"BFnbt0606667_CR17","doi-asserted-by":"publisher","first-page":"570","DOI":"10.1016\/j.tcb.2003.09.002","volume":"13","author":"BM Slepchenko","year":"2003","unstructured":"Slepchenko, B.M., Schaff, J.C., Macara, I. & Loew, L.M. Quantitative cell biology with the Virtual Cell. Trends Cell Biol. 13, 570\u2013576 (2003).","journal-title":"Trends Cell Biol."}],"container-title":["Nature Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/nbt0606-667.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nbt0606-667","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nbt0606-667.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,18]],"date-time":"2023-05-18T19:56:52Z","timestamp":1684439812000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/nbt0606-667"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,6]]},"references-count":17,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2006,6]]}},"alternative-id":["BFnbt0606667"],"URL":"https:\/\/doi.org\/10.1038\/nbt0606-667","relation":{},"ISSN":["1087-0156","1546-1696"],"issn-type":[{"value":"1087-0156","type":"print"},{"value":"1546-1696","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,6]]}}}