Modeling Biological Systems in Stochastic Concurrent Constraint Programming
We present an application of stochastic Concurrent Constraint Programming (sCCP) for modeling biological systems. We provide a library of sCCP processes that can be used to describe straightforwardly biological networks. In the meanwhile, we show that sCCP proves to be a general and extensible frame...
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| Published in: | Constraints : an international journal Vol. 13; no. 1-2; pp. 66 - 90 |
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| Format: | Journal Article |
| Language: | English |
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01.06.2008
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| ISSN: | 1383-7133, 1572-9354 |
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| Abstract | We present an application of stochastic Concurrent Constraint Programming (sCCP) for modeling biological systems. We provide a library of sCCP processes that can be used to describe straightforwardly biological networks. In the meanwhile, we show that sCCP proves to be a general and extensible framework, allowing to describe a wide class of dynamical behaviours and kinetic laws. |
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| AbstractList | We present an application of stochastic Concurrent Constraint Programming (sCCP) for modeling biological systems. We provide a library of sCCP processes that can be used to describe straightforwardly biological networks. In the meanwhile, we show that sCCP proves to be a general and extensible framework, allowing to describe a wide class of dynamical behaviours and kinetic laws. |
| Author | Bortolussi, Luca Policriti, Alberto |
| Author_xml | – sequence: 1 givenname: Luca surname: Bortolussi fullname: Bortolussi, Luca email: luca@dmi.units.it organization: Deparment of Mathematics and Computer Science, University of Trieste – sequence: 2 givenname: Alberto surname: Policriti fullname: Policriti, Alberto organization: Department of Mathematics and Computer Science, University of Udine |
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| Cites_doi | 10.1093/bib/5.3.259 10.7551/mitpress/3087.001.0001 10.1016/0304-3975(95)00047-Z 10.1017/CBO9780511810633 10.1093/bioinformatics/btg042 10.1016/j.entcs.2006.07.012 10.1063/1.481811 10.1007/3-540-45351-2_6 10.1109/BIBM.2007.31 10.1038/35002125 10.1089/10665270252833208 10.1021/j100540a008 10.1038/419343a 10.1073/pnas.93.19.10078 10.1091/mbc.10.8.2703 10.1007/11599128_10 10.1093/comjnl/38.7.578 10.7551/mitpress/2086.001.0001 10.1137/1.9780898719147 10.1093/bioinformatics/btl172 10.1016/0021-9991(76)90041-3 10.1109/QEST.2005.12 10.1016/S0020-0190(01)00214-9 10.1063/1.1545446 10.1145/99583.99627 10.1201/9781420010664 |
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| References | GillespieD. T.A general method for numerically simulating the stochastic time evolution of coupled chemical reactionsJournal of Computers in Physics19762240343410.1016/0021-9991(76)90041-3503370 RegevA.ShapiroE.Cellular abstractions: Cells as computationNature200241934310.1038/419343a Edelstein-Keshet, L. (2005). Mathematical models in biology. SIAM. 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. Gutiérrez, J., Perez, J. A., Rueda, C., & Valencia, F. D. (2006). Timed concurrent constraint programming for analyzing biological systems. In Proceedings of MeCBIC’06. PriamiC.Stochastic π-calculusComputer Journal199538657858910.1093/comjnl/38.7.578 Bortolussi, L., Fonda, S., & Policriti, A. (2007). Constraint-based simulation of biological systems described by molecular interaction maps. In Backofen, R., dal Palù, A., S. Will (Eds.), Proceeding of third international workshop on constraint-based methods in bioinformatics, WCB 2007 (pp. 1–9). Porto. HuangC. F.FerrellJ. T.Ultrasensitivity in the mitogen-activated protein kinase cascadePNAS, Biochemistry1996151100781008310.1073/pnas.93.19.10078 Bortolussi, L., & Policriti, A. (2006b). Relating stochastic process algebras and differential equations for biological modeling. In Proceedings of PASTA 2006. Imperial College Press. GillespieD. T.A rigorous derivation of the chemical master equationPhysica A199222403432503370 ShapiroB. E.LevchenkoA.MeyerowitzE. M.WoldB. J.MjolsnessE. D.Cellerator: Extending a computer algebra system to include biochemical arrows for signal transduction simulationsBioinformatics200319567767810.1093/bioinformatics/btg042 Bortolussi, L., & Policriti, A. (2006a). Modeling biological systems in concurrent constraint programming. In Dovier, A., dal Palù, A., Will, S., (Eds.), Proceedings of second international workshop on constraint-based methods in bioinformatics, WCB 2006 (pp. 6–29). Nantes. Bower, J. M., & Bolouri, H. (Eds.) (2000). Computational modeling of genetic and biochemical networks. MIT Press. Saraswat, V. A. (1993). Concurrent constraint programming. MIT press. Bortolussi, L. (2006). Stochastic concurrent constraint programming. In Proceedings of 4th international workshop on quantitative aspects of programming languages, QAPL 2006, ENTCS (Vol. 164, pp. 65–80). Norris, J. R. (1997). Markov Chains. Cambridge University Press. Cornish-Bowden, A. (2004). Fundamentals of chemical kinetics, 3rd edn. Portland Press. de Boer, F. S., Di Pierro, A., & Palamidessi, C. (1995). Nondeterminism and infinite computations in constraint programming. Theoretical Computer Science, 151(1). Hillston, J. (2005). Fluid flow approximation of pepa models. In Proceedings of the second international conference on the quantitative evaluation of systems (QEST05). 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. 19–32). KohnK. W.Molecular interaction map of the mammalian cell cycle control and dna repair systemsMolecular Biology of the Cell19991027032734 GillespieD. T.Exact stochastic simulation of coupled chemical reactionsJournal of Physical Chemistry197781252340236110.1021/j100540a008 De JongH.Modeling and simulation of genetic regulatory systems: A literature reviewJournal of Computational Biology2002916710310.1089/10665270252833208 PriamiC.QuagliaP.Modelling the dynamics of biosystemsBriefings in Bioinformatics20045325926910.1093/bib/5.3.259 Saraswat, V. A., Rinard, M., & Panangaden, P. (1991). Semantics foundations of concurrent constraint programming. In Proceedings of POPL. GillespieD.The chemical langevin equationJournal of Chemical Physics2000113129730610.1063/1.481811 PriamiC.RegevA.ShapiroE.Y.SilvermanW.Application of a stochastic name-passing calculus to representation and simulation of molecular processesInformation Processing Letters200180125310997.9201810.1016/S0020-0190(01)00214-91859381 RaoC. V.ArkinA. P.Stochastic chemical kinetics and the quasi-steady state assumption: Application to the gillespie algorithmJournal Chemical Physics2003118114999501010.1063/1.1545446 Voit, E. O. (2000). Computational analysis of biochemical systems. Cambridge University Press. VilarJ. M. G.Yuan KuehH.BarkaiN.LeiblerS.Mechanisms of noise resistance in genetic oscillatorsProceedings of the National Academy of Sciences of the United States of America2002999599110.1073/pnas.092133899 CardelliL.Abstract machines of systems biologyTransactions on Computational Systems Biology, III, LNBI2005373714516810.1007/11599128_10 CalzoneL.FagesF.SolimanS.Biocham: an environment for modeling biological systems and formalizing experimental knowledgeBioinformatics2006221805180710.1093/bioinformatics/btl172 ElowitzM. B.LeiblerS.A synthetic oscillatory network of transcriptional regulatorsNature200040333533810.1038/35002125 Henkin, L., Monk, J. D., & Tarski, A. (1971). Cylindric algebras, Part I. North-Holland. Wilkinson, D. J. (2006). Stochastic modelling for systems biology. Chapman & Hall. Cardelli, L., & Phillips, A. (2004). A correct abstract machine for the stochastic pi-calculus. In Proceeding of Bioconcur 2004. Swedish Institute for Computer Science (2007). Sicstus prolog home page. Swedish Institute for Computer Science Gillespie, D., & Petzold, L. (2006). System modelling in cellular biology. Chapter Numerical Simulation for Biochemical Kinetics. MIT Press. Kitano, H. (2001). Foundations of systems biology. MIT Press. BlosseyR.CardelliL.PhillipsA.A compositional approach to the stochastic dynamics of gene networksTransaction Computer System Biology200639399912210.1007/11732488_102298401 9034_CR4 9034_CR5 C. V. Rao (9034_CR33) 2003; 118 9034_CR3 9034_CR1 C. Priami (9034_CR30) 1995; 38 L. Calzone (9034_CR9) 2006; 22 C. F. Huang (9034_CR26) 1996; 151 K. W. Kohn (9034_CR28) 1999; 10 9034_CR36 9034_CR13 9034_CR35 9034_CR15 H. Jong De (9034_CR14) 2002; 9 9034_CR17 9034_CR39 A. Regev (9034_CR34) 2002; 419 9034_CR19 D. T. Gillespie (9034_CR20) 1992; 22 D. T. Gillespie (9034_CR21) 1976; 22 9034_CR12 9034_CR11 D. Gillespie (9034_CR18) 2000; 113 C. Priami (9034_CR32) 2001; 80 M. B. Elowitz (9034_CR16) 2000; 403 9034_CR25 9034_CR24 9034_CR27 9034_CR29 B. E. Shapiro (9034_CR37) 2003; 19 R. Blossey (9034_CR2) 2006; 3939 D. T. Gillespie (9034_CR22) 1977; 81 L. Cardelli (9034_CR10) 2005; 3737 J. M. G. Vilar (9034_CR38) 2002; 99 9034_CR40 9034_CR8 9034_CR6 9034_CR23 C. Priami (9034_CR31) 2004; 5 9034_CR7 |
| References_xml | – reference: PriamiC.RegevA.ShapiroE.Y.SilvermanW.Application of a stochastic name-passing calculus to representation and simulation of molecular processesInformation Processing Letters200180125310997.9201810.1016/S0020-0190(01)00214-91859381 – reference: RegevA.ShapiroE.Cellular abstractions: Cells as computationNature200241934310.1038/419343a – reference: CalzoneL.FagesF.SolimanS.Biocham: an environment for modeling biological systems and formalizing experimental knowledgeBioinformatics2006221805180710.1093/bioinformatics/btl172 – reference: Gutiérrez, J., Perez, J. A., Rueda, C., & Valencia, F. D. (2006). Timed concurrent constraint programming for analyzing biological systems. In Proceedings of MeCBIC’06. – reference: Cornish-Bowden, A. (2004). Fundamentals of chemical kinetics, 3rd edn. Portland Press. – reference: Saraswat, V. A. (1993). Concurrent constraint programming. MIT press. – reference: de Boer, F. S., Di Pierro, A., & Palamidessi, C. (1995). Nondeterminism and infinite computations in constraint programming. Theoretical Computer Science, 151(1). – reference: Swedish Institute for Computer Science (2007). Sicstus prolog home page. Swedish Institute for Computer Science – reference: GillespieD. T.A rigorous derivation of the chemical master equationPhysica A199222403432503370 – reference: Kitano, H. (2001). Foundations of systems biology. MIT Press. – reference: 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. – reference: Bortolussi, L., & Policriti, A. (2006a). Modeling biological systems in concurrent constraint programming. In Dovier, A., dal Palù, A., Will, S., (Eds.), Proceedings of second international workshop on constraint-based methods in bioinformatics, WCB 2006 (pp. 6–29). Nantes. – reference: GillespieD. T.Exact stochastic simulation of coupled chemical reactionsJournal of Physical Chemistry197781252340236110.1021/j100540a008 – reference: Saraswat, V. A., Rinard, M., & Panangaden, P. (1991). Semantics foundations of concurrent constraint programming. In Proceedings of POPL. – reference: PriamiC.Stochastic π-calculusComputer Journal199538657858910.1093/comjnl/38.7.578 – reference: VilarJ. M. G.Yuan KuehH.BarkaiN.LeiblerS.Mechanisms of noise resistance in genetic oscillatorsProceedings of the National Academy of Sciences of the United States of America2002999599110.1073/pnas.092133899 – reference: Wilkinson, D. J. (2006). Stochastic modelling for systems biology. Chapman & Hall. – reference: KohnK. W.Molecular interaction map of the mammalian cell cycle control and dna repair systemsMolecular Biology of the Cell19991027032734 – reference: Bortolussi, L., Fonda, S., & Policriti, A. (2007). Constraint-based simulation of biological systems described by molecular interaction maps. In Backofen, R., dal Palù, A., S. Will (Eds.), Proceeding of third international workshop on constraint-based methods in bioinformatics, WCB 2007 (pp. 1–9). Porto. – reference: Henkin, L., Monk, J. D., & Tarski, A. (1971). Cylindric algebras, Part I. North-Holland. – reference: Hillston, J. (2005). Fluid flow approximation of pepa models. In Proceedings of the second international conference on the quantitative evaluation of systems (QEST05). – reference: ElowitzM. B.LeiblerS.A synthetic oscillatory network of transcriptional regulatorsNature200040333533810.1038/35002125 – reference: GillespieD.The chemical langevin equationJournal of Chemical Physics2000113129730610.1063/1.481811 – reference: Bower, J. M., & Bolouri, H. (Eds.) (2000). Computational modeling of genetic and biochemical networks. MIT Press. – reference: Cardelli, L., & Phillips, A. (2004). A correct abstract machine for the stochastic pi-calculus. In Proceeding of Bioconcur 2004. – reference: Bortolussi, L., & Policriti, A. (2006b). Relating stochastic process algebras and differential equations for biological modeling. In Proceedings of PASTA 2006. Imperial College Press. – reference: Edelstein-Keshet, L. (2005). Mathematical models in biology. SIAM. – reference: BlosseyR.CardelliL.PhillipsA.A compositional approach to the stochastic dynamics of gene networksTransaction Computer System Biology200639399912210.1007/11732488_102298401 – reference: Norris, J. R. (1997). Markov Chains. Cambridge University Press. – reference: HuangC. F.FerrellJ. T.Ultrasensitivity in the mitogen-activated protein kinase cascadePNAS, Biochemistry1996151100781008310.1073/pnas.93.19.10078 – reference: GillespieD. T.A general method for numerically simulating the stochastic time evolution of coupled chemical reactionsJournal of Computers in Physics19762240343410.1016/0021-9991(76)90041-3503370 – reference: RaoC. V.ArkinA. P.Stochastic chemical kinetics and the quasi-steady state assumption: Application to the gillespie algorithmJournal Chemical Physics2003118114999501010.1063/1.1545446 – reference: CardelliL.Abstract machines of systems biologyTransactions on Computational Systems Biology, III, LNBI2005373714516810.1007/11599128_10 – reference: PriamiC.QuagliaP.Modelling the dynamics of biosystemsBriefings in Bioinformatics20045325926910.1093/bib/5.3.259 – reference: 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. 19–32). – reference: ShapiroB. E.LevchenkoA.MeyerowitzE. M.WoldB. J.MjolsnessE. D.Cellerator: Extending a computer algebra system to include biochemical arrows for signal transduction simulationsBioinformatics200319567767810.1093/bioinformatics/btg042 – reference: Bortolussi, L. (2006). Stochastic concurrent constraint programming. In Proceedings of 4th international workshop on quantitative aspects of programming languages, QAPL 2006, ENTCS (Vol. 164, pp. 65–80). – reference: Gillespie, D., & Petzold, L. (2006). System modelling in cellular biology. Chapter Numerical Simulation for Biochemical Kinetics. MIT Press. – reference: De JongH.Modeling and simulation of genetic regulatory systems: A literature reviewJournal of Computational Biology2002916710310.1089/10665270252833208 – reference: Voit, E. O. (2000). Computational analysis of biochemical systems. 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| Snippet | We present an application of stochastic Concurrent Constraint Programming (sCCP) for modeling biological systems. We provide a library of sCCP processes that... |
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| StartPage | 66 |
| SubjectTerms | Artificial Intelligence Computer Science Operations Research/Decision Theory Optimization |
| Title | Modeling Biological Systems in Stochastic Concurrent Constraint Programming |
| URI | https://link.springer.com/article/10.1007/s10601-007-9034-8 |
| Volume | 13 |
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