{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T10:55:55Z","timestamp":1742381755487},"publisher-location":"Berlin, Heidelberg","reference-count":23,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540688921"},{"type":"electronic","value":"9783540688945"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"DOI":"10.1007\/978-3-540-68894-5_5","type":"book-chapter","created":{"date-parts":[[2008,5,30]],"date-time":"2008-05-30T08:39:25Z","timestamp":1212136765000},"page":"125-167","source":"Crossref","is-referenced-by-count":20,"title":["Simulation Methods in Systems Biology"],"prefix":"10.1007","author":[{"given":"Daniel T.","family":"Gillespie","sequence":"first","affiliation":[]}],"member":"297","reference":[{"key":"5_CR1","doi-asserted-by":"publisher","first-page":"1735","DOI":"10.1007\/978-1-4020-3286-8_86","volume-title":"Handbook of Materials Modeling","author":"D. Gillespie","year":"2005","unstructured":"Gillespie, D.: Stochastic chemical kinetics. In: Yip, S. (ed.) Handbook of Materials Modeling, pp. 1735\u20131752. Springer, Heidelberg (2005)"},{"key":"5_CR2","doi-asserted-by":"crossref","first-page":"331","DOI":"10.7551\/mitpress\/9780262195485.003.0016","volume-title":"System Modeling in Cellular Biology","author":"D. Gillespie","year":"2006","unstructured":"Gillespie, D., Petzold, L.: Numerical simulation for biochemical kinetics. In: Szallasi, Z., Stelling, J., Periwal, V. (eds.) System Modeling in Cellular Biology, pp. 331\u2013353. MIT Press, Cambridge (2006)"},{"key":"5_CR3","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1146\/annurev.physchem.58.032806.104637","volume":"58","author":"D. Gillespie","year":"2007","unstructured":"Gillespie, D.: Stochastic simulation of chemical kinetics. Ann. Rev. Phys. Chem.\u00a058, 35\u201355 (2007)","journal-title":"Ann. Rev. Phys. Chem."},{"key":"5_CR4","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1016\/0378-4371(92)90283-V","volume":"188","author":"D. Gillespie","year":"1992","unstructured":"Gillespie, D.: A rigorous derivation of the chemical master equation. Physica A\u00a0188, 404\u2013425 (1992)","journal-title":"Physica A"},{"key":"5_CR5","unstructured":"Gillespie, D.: Markov Processes: An Introduction for Physical Scientists. Academic (1992)"},{"key":"5_CR6","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1119\/1.18210","volume":"64","author":"D. Gillespie","year":"1996","unstructured":"Gillespie, D.: The mathematics of Brownian motion and Johnson noise. Am. J. Phys.\u00a064, 225\u2013240 (1996)","journal-title":"Am. J. Phys."},{"key":"5_CR7","doi-asserted-by":"publisher","first-page":"1246","DOI":"10.1119\/1.18387","volume":"64","author":"D. Gillespie","year":"1996","unstructured":"Gillespie, D.: The multivariate Langevin and Fokker-Planck equations. Am. J. Phys.\u00a064, 1246\u20131257 (1996)","journal-title":"Am. J. Phys."},{"key":"5_CR8","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1063\/1.481811","volume":"113","author":"D. Gillespie","year":"2000","unstructured":"Gillespie, D.: The chemical Langevin equation. J. Chem. Phys.\u00a0113, 297\u2013306 (2000)","journal-title":"J. Chem. Phys."},{"key":"5_CR9","doi-asserted-by":"publisher","first-page":"5063","DOI":"10.1021\/jp0128832","volume":"106","author":"D. Gillespie","year":"2002","unstructured":"Gillespie, D.: The chemical Langevin and Fokker-Planck equations for the reversible isomerization reaction. J. Phys. Chem. A\u00a0106, 5063\u20135071 (2002)","journal-title":"J. Phys. Chem. A"},{"key":"5_CR10","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1038\/nbt1054","volume":"23","author":"L. Lok","year":"2005","unstructured":"Lok, L., Brent, R.: Automatic generation of cellular reaction networks with Moleculizer 1. 0. Nature Biotechnology\u00a023, 131\u2013136 (2005)","journal-title":"Nature Biotechnology"},{"key":"5_CR11","doi-asserted-by":"publisher","first-page":"1716","DOI":"10.1063\/1.1378322","volume":"115","author":"D. Gillespie","year":"2001","unstructured":"Gillespie, D.: Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys.\u00a0115, 1716\u20131733 (2001)","journal-title":"J. Chem. Phys."},{"key":"5_CR12","doi-asserted-by":"publisher","first-page":"8229","DOI":"10.1063\/1.1613254","volume":"119","author":"D. Gillespie","year":"2003","unstructured":"Gillespie, D., Petzold, L.: Improved leap-size selection for accelerated stochastic simulation. J. Chem. Phys.\u00a0119, 8229\u20138234 (2003)","journal-title":"J. Chem. Phys."},{"key":"5_CR13","doi-asserted-by":"publisher","first-page":"44109","DOI":"10.1063\/1.2159468","volume":"124","author":"Y. Cao","year":"2006","unstructured":"Cao, Y., Gillespie, D., Petzold, L.: Efficient step size selection for the tau-leaping simulation method. J. Chem. Phys.\u00a0124, 044109 (2006)","journal-title":"J. Chem. Phys."},{"key":"5_CR14","doi-asserted-by":"publisher","first-page":"54104","DOI":"10.1063\/1.1992473","volume":"123","author":"Y. Cao","year":"2005","unstructured":"Cao, Y., Gillespie, D., Petzold, L.: Avoiding negative populations in explicit Poisson tau-leaping. J. Chem. Phys.\u00a0123, 054104 (2005)","journal-title":"J. Chem. Phys."},{"key":"5_CR15","doi-asserted-by":"publisher","first-page":"12784","DOI":"10.1063\/1.1627296","volume":"119","author":"M. Rathinam","year":"2003","unstructured":"Rathinam, M., Petzold, L., Cao, Y., Gillespie, D.: Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method. J. Chem. Phys.\u00a0119, 12784\u201312794 (2003)","journal-title":"J. Chem. Phys."},{"key":"5_CR16","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1137\/040603206","volume":"4","author":"M. Rathinam","year":"2005","unstructured":"Rathinam, M., Petzold, L., Cao, Y., Gillespie, D.: Consistency and stability of tau-leaping schemes for chemical reaction systems. Multiscale Model. Simul.\u00a04, 867\u2013895 (2005)","journal-title":"Multiscale Model. Simul."},{"key":"5_CR17","doi-asserted-by":"crossref","unstructured":"Ascher, M., Petzold, L.: Computer Methods for Ordinary Differential Equations and Differential Algebraic Equations. In: SIAM (1998)","DOI":"10.1137\/1.9781611971392"},{"key":"5_CR18","doi-asserted-by":"publisher","first-page":"14116","DOI":"10.1063\/1.1824902","volume":"122","author":"Y. Cao","year":"2005","unstructured":"Cao, Y., Gillespie, D., Petzold, L.: The slow-scale stochastic simulation algorithm. J. Chem. Phys.\u00a0122, 014116 (2005)","journal-title":"J. Chem. Phys."},{"key":"5_CR19","doi-asserted-by":"publisher","first-page":"144917","DOI":"10.1063\/1.2052596","volume":"123","author":"Y. Cao","year":"2005","unstructured":"Cao, Y., Gillespie, D., Petzold, L.: Accelerated stochastic simulation of the stiff enzyme-substrate reaction. J. Chem. Phys.\u00a0123, 144917 (2005)","journal-title":"J. Chem. Phys."},{"key":"5_CR20","doi-asserted-by":"crossref","first-page":"0194107","DOI":"10.1063\/1.2109987","volume":"123","author":"D. Gillespie","year":"2005","unstructured":"Gillespie, D., Petzold, L., Cao, Y.: Comment on Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates. (J. Chem. Phys.\u00a0123, 0194107 (2005)); J. Chem. Phys. 126, 0137101 (2007)","journal-title":"J. Chem. Phys."},{"key":"5_CR21","doi-asserted-by":"publisher","first-page":"194107","DOI":"10.1063\/1.2109987","volume":"123","author":"E.W. Liu","year":"2005","unstructured":"Liu, E.W., Vanden-Eijnden, D., Nested, E.: stochastic simulation algorithm for chemical kinetic systems with disparate rates. J. Chem. Phys.\u00a0123, 194107 (2005)","journal-title":"J. Chem. Phys."},{"key":"5_CR22","doi-asserted-by":"publisher","first-page":"224101","DOI":"10.1063\/1.2745299","volume":"126","author":"Y. Cao","year":"2007","unstructured":"Cao, Y., Gillespie, D., Petzold, L.: Adaptive explicit-implicit tau-leaping with automatic tau-selection. J. Chem. Phys.\u00a0126, 224101 (2007)","journal-title":"J. Chem. Phys."},{"key":"5_CR23","doi-asserted-by":"publisher","first-page":"34302","DOI":"10.1063\/1.2424461","volume":"126","author":"D. Gillespie","year":"2007","unstructured":"Gillespie, D., Lampoudi, S., Petzold, L.: Effect of reactant size on discrete stochastic chemical kinetics. J. Chem. Phys.\u00a0126, 034302 (2007)","journal-title":"J. Chem. Phys."}],"container-title":["Lecture Notes in Computer Science","Formal Methods for Computational Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-68894-5_5.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,5,3]],"date-time":"2021-05-03T00:18:12Z","timestamp":1620001092000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-68894-5_5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[null]]},"ISBN":["9783540688921","9783540688945"],"references-count":23,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-68894-5_5","relation":{},"subject":[]}}