{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T19:50:04Z","timestamp":1762458604886},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"1-2","license":[{"start":{"date-parts":[[2008,1,30]],"date-time":"2008-01-30T00:00:00Z","timestamp":1201651200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Constraints"],"published-print":{"date-parts":[[2008,6]]},"DOI":"10.1007\/s10601-007-9034-8","type":"journal-article","created":{"date-parts":[[2008,1,29]],"date-time":"2008-01-29T07:02:30Z","timestamp":1201590150000},"page":"66-90","source":"Crossref","is-referenced-by-count":37,"title":["Modeling Biological Systems in Stochastic Concurrent Constraint Programming"],"prefix":"10.1007","volume":"13","author":[{"given":"Luca","family":"Bortolussi","sequence":"first","affiliation":[]},{"given":"Alberto","family":"Policriti","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2008,1,30]]},"reference":[{"key":"9034_CR1","doi-asserted-by":"crossref","unstructured":"Alur, R., Belta, C., Ivancic, F., Kumar, V., Mintz, M., Pappas, G., et al. (2001). Hybrid modeling and simulation of biomolecular networks. In Proceedings of fourth international workshop on hybrid systems: Computation and control, LNCS 2034 (pp.\u00a019\u201332).","DOI":"10.1007\/3-540-45351-2_6"},{"key":"9034_CR2","first-page":"99","volume":"3939","author":"R. Blossey","year":"2006","unstructured":"Blossey, R., Cardelli, L., & Phillips, A. (2006). A compositional approach to the stochastic dynamics of gene networks. Transaction Computer System Biology, 3939, 99\u2013122.","journal-title":"Transaction Computer System Biology"},{"key":"9034_CR3","doi-asserted-by":"crossref","unstructured":"Bortolussi, L. (2006). Stochastic concurrent constraint programming. In Proceedings of 4th international workshop on quantitative aspects of programming languages, QAPL 2006, ENTCS (Vol.\u00a0164, pp.\u00a065\u201380).","DOI":"10.1016\/j.entcs.2006.07.012"},{"key":"9034_CR4","unstructured":"Bortolussi, L. (2007). Constraint-based approaches to stochastic dynamics of biological systems. Ph.D. thesis, Ph.D. in Computer Science, University of Udine, http:\/\/www.dmi.units.it\/~bortolu\/files\/reps\/Bortolussi-PhDThesis.pdf ."},{"key":"9034_CR5","doi-asserted-by":"crossref","unstructured":"Bortolussi, L., Fonda, S., & Policriti, A. (2007). Constraint-based simulation of biological systems described by molecular interaction maps. In Backofen, R., dal Pal\u00f9, A., S. Will (Eds.), Proceeding of third international workshop on constraint-based methods in bioinformatics, WCB 2007 (pp.\u00a01\u20139). Porto.","DOI":"10.1109\/BIBM.2007.31"},{"key":"9034_CR6","unstructured":"Bortolussi, L., & Policriti, A. (2006a). Modeling biological systems in concurrent constraint programming. In Dovier, A., dal\u00a0Pal\u00f9, A., Will, S., (Eds.), Proceedings of second international workshop on constraint-based methods in bioinformatics, WCB 2006 (pp.\u00a06\u201329). Nantes."},{"key":"9034_CR7","unstructured":"Bortolussi, L., & Policriti, A. (2006b). Relating stochastic process algebras and differential equations for biological modeling. In Proceedings of PASTA 2006. Imperial College Press."},{"key":"9034_CR8","unstructured":"Bower, J. M., & Bolouri, H. (Eds.) (2000). Computational modeling of genetic and biochemical networks. MIT Press."},{"key":"9034_CR9","doi-asserted-by":"crossref","first-page":"1805","DOI":"10.1093\/bioinformatics\/btl172","volume":"22","author":"L. Calzone","year":"2006","unstructured":"Calzone, L., Fages, F., & Soliman, S. (2006). Biocham: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics, 22, 1805\u20131807.","journal-title":"Bioinformatics"},{"key":"9034_CR10","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1007\/11599128_10","volume":"3737","author":"L. Cardelli","year":"2005","unstructured":"Cardelli, L. (2005). Abstract machines of systems biology. Transactions on Computational Systems Biology, III, LNBI, 3737, 145\u2013168.","journal-title":"Transactions on Computational Systems Biology, III, LNBI"},{"key":"9034_CR11","unstructured":"Cardelli, L., & Phillips, A. (2004). A correct abstract machine for the stochastic pi-calculus. In Proceeding of Bioconcur 2004."},{"key":"9034_CR12","unstructured":"Cornish-Bowden, A. (2004). Fundamentals of chemical kinetics, 3rd edn. Portland Press."},{"key":"9034_CR13","doi-asserted-by":"crossref","unstructured":"de\u00a0Boer, F. S., Di\u00a0Pierro, A., & Palamidessi, C. (1995). Nondeterminism and infinite computations in constraint programming. Theoretical Computer Science, 151(1).","DOI":"10.1016\/0304-3975(95)00047-Z"},{"issue":"1","key":"9034_CR14","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1089\/10665270252833208","volume":"9","author":"H. Jong De","year":"2002","unstructured":"De Jong, H. (2002). Modeling and simulation of genetic regulatory systems: A literature review. Journal of Computational Biology, 9(1), 67\u2013103.","journal-title":"Journal of Computational Biology"},{"key":"9034_CR15","doi-asserted-by":"crossref","unstructured":"Edelstein-Keshet, L. (2005). Mathematical models in biology. SIAM.","DOI":"10.1137\/1.9780898719147"},{"key":"9034_CR16","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/35002125","volume":"403","author":"M. B. Elowitz","year":"2000","unstructured":"Elowitz, M. B., & Leibler, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature, 403, 335\u2013338.","journal-title":"Nature"},{"key":"9034_CR17","unstructured":"Swedish\u00a0Institute for Computer\u00a0Science (2007). Sicstus prolog home page. Swedish\u00a0Institute for Computer\u00a0Science"},{"issue":"1","key":"9034_CR18","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1063\/1.481811","volume":"113","author":"D. Gillespie","year":"2000","unstructured":"Gillespie, D. (2000). The chemical langevin equation. Journal of Chemical Physics, 113(1), 297\u2013306","journal-title":"Journal of Chemical Physics"},{"key":"9034_CR19","unstructured":"Gillespie, D., & Petzold, L. (2006). System modelling in cellular biology. Chapter Numerical Simulation for Biochemical Kinetics. MIT Press."},{"key":"9034_CR20","first-page":"403","volume":"22","author":"D. T. Gillespie","year":"1992","unstructured":"Gillespie, D. T. (1992). A rigorous derivation of the chemical master equation. Physica A, 22, 403\u2013432.","journal-title":"Physica A"},{"key":"9034_CR21","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/0021-9991(76)90041-3","volume":"22","author":"D. T. Gillespie","year":"1976","unstructured":"Gillespie, D. T. (1976). A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computers in Physics, 22, 403\u2013434","journal-title":"Journal of Computers in Physics"},{"issue":"25","key":"9034_CR22","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1021\/j100540a008","volume":"81","author":"D. T. Gillespie","year":"1977","unstructured":"Gillespie, D. T. (1977). Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry, 81(25), 2340\u20132361","journal-title":"Journal of Physical Chemistry"},{"key":"9034_CR23","unstructured":"Guti\u00e9rrez, J., Perez, J. A., Rueda, C., & Valencia, F. D. (2006). Timed concurrent constraint programming for analyzing biological systems. In Proceedings of MeCBIC\u201906."},{"key":"9034_CR24","unstructured":"Henkin, L., Monk, J. D., & Tarski, A. (1971). Cylindric algebras, Part I. North-Holland."},{"key":"9034_CR25","doi-asserted-by":"crossref","unstructured":"Hillston, J. (2005). Fluid flow approximation of pepa models. In Proceedings of the second international conference on the quantitative evaluation of systems (QEST05).","DOI":"10.1109\/QEST.2005.12"},{"key":"9034_CR26","doi-asserted-by":"crossref","first-page":"10078","DOI":"10.1073\/pnas.93.19.10078","volume":"151","author":"C. F. Huang","year":"1996","unstructured":"Huang, C. F., & Ferrell, J. T. (1996). Ultrasensitivity in the mitogen-activated protein kinase cascade. PNAS, Biochemistry, 151, 10078\u201310083.","journal-title":"PNAS, Biochemistry"},{"key":"9034_CR27","doi-asserted-by":"crossref","unstructured":"Kitano, H. (2001). Foundations of systems biology. MIT Press.","DOI":"10.7551\/mitpress\/3087.001.0001"},{"key":"9034_CR28","doi-asserted-by":"crossref","first-page":"2703","DOI":"10.1091\/mbc.10.8.2703","volume":"10","author":"K. W. Kohn","year":"1999","unstructured":"Kohn, K. W. (1999). Molecular interaction map of the mammalian cell cycle control and dna repair systems. Molecular Biology of the Cell, 10, 2703\u20132734.","journal-title":"Molecular Biology of the Cell"},{"key":"9034_CR29","doi-asserted-by":"crossref","unstructured":"Norris, J. R. (1997). Markov Chains. Cambridge University Press.","DOI":"10.1017\/CBO9780511810633"},{"issue":"6","key":"9034_CR30","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1093\/comjnl\/38.7.578","volume":"38","author":"C. Priami","year":"1995","unstructured":"Priami, C. (1995). Stochastic \u03c0-calculus. Computer Journal, 38(6), 578\u2013589.","journal-title":"Computer Journal"},{"issue":"3","key":"9034_CR31","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1093\/bib\/5.3.259","volume":"5","author":"C. Priami","year":"2004","unstructured":"Priami, C., & Quaglia, P. (2004). Modelling the dynamics of biosystems. Briefings in Bioinformatics, 5(3), 259\u2013269.","journal-title":"Briefings in Bioinformatics"},{"issue":"1","key":"9034_CR32","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/S0020-0190(01)00214-9","volume":"80","author":"C. Priami","year":"2001","unstructured":"Priami, C., Regev, A., Shapiro, E. Y., & Silverman, W. (2001). Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters, 80(1), 25\u201331.","journal-title":"Information Processing Letters"},{"issue":"11","key":"9034_CR33","doi-asserted-by":"crossref","first-page":"4999","DOI":"10.1063\/1.1545446","volume":"118","author":"C. V. Rao","year":"2003","unstructured":"Rao, C. V., & Arkin, A. P. (2003). Stochastic chemical kinetics and the quasi-steady state assumption: Application to the gillespie algorithm. Journal Chemical Physics, 118(11), 4999\u20135010.","journal-title":"Journal Chemical Physics"},{"key":"9034_CR34","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/419343a","volume":"419","author":"A. Regev","year":"2002","unstructured":"Regev, A., & Shapiro, E. (2002). Cellular abstractions: Cells as computation. Nature, 419, 343.","journal-title":"Nature"},{"key":"9034_CR35","doi-asserted-by":"crossref","unstructured":"Saraswat, V. A. (1993). Concurrent constraint programming. MIT press.","DOI":"10.7551\/mitpress\/2086.001.0001"},{"key":"9034_CR36","doi-asserted-by":"crossref","unstructured":"Saraswat, V. A., Rinard, M., & Panangaden, P. (1991). Semantics foundations of concurrent constraint programming. In Proceedings of POPL.","DOI":"10.1145\/99583.99627"},{"issue":"5","key":"9034_CR37","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1093\/bioinformatics\/btg042","volume":"19","author":"B. E. Shapiro","year":"2003","unstructured":"Shapiro, B. E., Levchenko, A., Meyerowitz, E. M., Wold\u00a0B. J., & Mjolsness, E. D. (2003). Cellerator: Extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinformatics, 19(5), 677\u2013678.","journal-title":"Bioinformatics"},{"issue":"9","key":"9034_CR38","first-page":"5991","volume":"99","author":"J. M. G. Vilar","year":"2002","unstructured":"Vilar, J. M.\u00a0G., Yuan\u00a0Kueh, H., Barkai, N., & Leibler, S. (2002). Mechanisms of noise resistance in genetic oscillators. Proceedings of the National Academy of Sciences of the United States of America, 99(9), 5991.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"9034_CR39","unstructured":"Voit, E. O. (2000). Computational analysis of biochemical systems. Cambridge University Press."},{"key":"9034_CR40","doi-asserted-by":"crossref","unstructured":"Wilkinson, D. J. (2006). Stochastic modelling for systems biology. Chapman & Hall.","DOI":"10.1201\/9781420010664"}],"container-title":["Constraints"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10601-007-9034-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10601-007-9034-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10601-007-9034-8","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T22:18:02Z","timestamp":1630621082000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10601-007-9034-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,1,30]]},"references-count":40,"journal-issue":{"issue":"1-2","published-print":{"date-parts":[[2008,6]]}},"alternative-id":["9034"],"URL":"https:\/\/doi.org\/10.1007\/s10601-007-9034-8","relation":{},"ISSN":["1383-7133","1572-9354"],"issn-type":[{"value":"1383-7133","type":"print"},{"value":"1572-9354","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,1,30]]}}}