{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,7]],"date-time":"2024-09-07T09:25:08Z","timestamp":1725701108628},"publisher-location":"Berlin, Heidelberg","reference-count":50,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540929093"},{"type":"electronic","value":"9783540929109"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012]]},"DOI":"10.1007\/978-3-540-92910-9_54","type":"book-chapter","created":{"date-parts":[[2012,8,25]],"date-time":"2012-08-25T10:54:06Z","timestamp":1345892046000},"page":"1835-1862","source":"Crossref","is-referenced-by-count":3,"title":["Algorithmic Systems Biology \u2014 Computer Science Propels Systems Biology"],"prefix":"10.1007","author":[{"given":"Corrado","family":"Priami","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"issue":"20","key":"54_CR00541","doi-asserted-by":"publisher","first-page":"3873","DOI":"10.1093\/bioinformatics\/bti624","volume":"21","author":"K Bashi","year":"2005","unstructured":"Bashi K, Forrest A, Ramanathan M (2005) SPLINDID: a semi-parametric, model-based method for obtaining transcription rates and gene regulation parameters from genomic and proteomic expression profiles. Bioinformatics 21(20):3873\u20133879","journal-title":"Bioinformatics"},{"volume-title":"Handbook of process algebras","year":"2001","key":"54_CR00542","unstructured":"Bergstra J, Ponse A, Smolka S (eds.) (2001) Handbook of process algebras. Elsevier, Amsterdam, The Netherlands"},{"volume-title":"Lecture notes in computer science","year":"2008","key":"54_CR00543","unstructured":"Bernardo M, Degano P, Zavattaro G (eds) (2008) Formal methods for computational systems biology. Lecture notes in computer science, vol 5016. Springer, New York"},{"key":"54_CR00544","volume-title":"Statistics and computing","author":"RJ Boys","year":"2008","unstructured":"Boys RJ, Wilkinson DJ, Kirkwood TB (2008) Bayesian inference for a discretely observed stochastic kinetic model. In: Statistics and computing. Springer, The Netherlands"},{"key":"54_CR00545","first-page":"257","volume-title":"CMSB 2004, Paris, France, May 2004. Lecture notes in computer science","author":"L Cardelli","year":"2005","unstructured":"Cardelli L (2005) Brane calculi-interactions of biological membranes. In: CMSB 2004, Paris, France, May 2004. Lecture notes in computer science, vol 3082. Springer, Berlin, pp 257\u2013280"},{"key":"54_CR00546","volume-title":"On the computational power of biochemistry","author":"L Cardelli","year":"2008","unstructured":"Cardelli L, Zavattaro G (2008) On the computational power of biochemistry. In: AB08, Austria, July\u2013 August 2008"},{"key":"54_CR00547","volume-title":"International research and development in systems biology","author":"M Cassman","year":"2005","unstructured":"Cassman M, Arkin A, Doyle F, Katagiri F, Lauffenburg D, Stokes C (2005) International research and development in systems biology. WTEC Panel on Systems Biology final report"},{"key":"54_CR00548","doi-asserted-by":"crossref","unstructured":"Chou IC, Martens H, Voit EO (2006) Parameter estimation in biochemical systems models with alternating regression. Theor Biol Med Model 3(25)","DOI":"10.1186\/1742-4682-3-25"},{"key":"54_CR00549","series-title":"Lecture notes in computer science","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1007\/978-3-540-68894-5_8","volume-title":"Calculi for biological systems","author":"F Ciocchetta","year":"2008","unstructured":"Ciocchetta F, Hillston J (2008) Calculi for biological systems. In: SFM-08, Bertinoro, Italy, June 2008. Lecture notes in computer science, vol 5016. Springer, pp 265\u2013312"},{"key":"54_CR005410","doi-asserted-by":"crossref","unstructured":"Ciocchetta F, Gilmore S, Guerriero M, Hillston J (2008a) Integrated simulation and model-checking for the analysis of biochemical systems. In: Proceedings of PASM 2008. Electr Notes Theor Comput Sci 238:17\u201338","DOI":"10.1016\/j.entcs.2009.02.048"},{"issue":"1","key":"54_CR005411","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1109\/TCBB.2007.70219","volume":"5","author":"F Ciocchetta","year":"2008","unstructured":"Ciocchetta F, Priami C, Quaglia P (2008b) An automatic translation of SBML into beta-binders. IEEE\/ACM Trans Comput Biol Bioinform 5(1):80\u201390","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"1","key":"54_CR005412","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/j.tcs.2004.03.065","volume":"325","author":"V Danos","year":"2004","unstructured":"Danos V, Laneve C (2004) Formal molecular biology. TCS 325(1):69\u2013110","journal-title":"TCS"},{"key":"54_CR005414","volume-title":"Scalable simulation of cellular signaling networks","author":"V Danos","year":"2007","unstructured":"Danos V, Feret J, Fontana W, Krivine J (2007) Scalable simulation of cellular signaling networks. In: Proceedings of APLAS\u201907, Singapore, November\u2013 December 2007"},{"key":"54_CR005415","series-title":"Lecture notes in computer science","doi-asserted-by":"crossref","DOI":"10.1007\/3-540-44804-7","volume-title":"Compositional methods for probabilistic systems","author":"L de Alfaro","year":"2001","unstructured":"de Alfaro L, Henzinger TA, Jhala R (2001) Compositional methods for probabilistic systems. In: CONCUR 2001, Aalborg, Denmark, August 2001. Lecture notes in computer science, vol 2154"},{"key":"54_CR005416","series-title":"Lecture notes in computer science","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1007\/978-3-540-88562-7_16","volume-title":"On parallel stochastic simulation of diffusive systems","author":"L Dematt\u00e9","year":"2008","unstructured":"Dematt\u00e9 L, Mazza T (2008) On parallel stochastic simulation of diffusive systems. In: Proceedings of CMSB2008, Rostock, Germany, October 2008. Lecture notes in computer science, vol 5307. Springer, pp 191\u2013210"},{"issue":"5","key":"54_CR005417","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1093\/bib\/bbn023","volume":"9","author":"L Dematt\u00e9","year":"2008","unstructured":"Dematt\u00e9 L, Priami C, Romanel A (2008a) The beta workbench: a tool to study the dynamics of biological systems. Brief Bioinform 9(5):437\u2013449","journal-title":"Brief Bioinform"},{"key":"54_CR005418","doi-asserted-by":"crossref","unstructured":"Dematt\u00e9 L, Priami C, Romanel A (2008b) The BlenX language: a tutorial. In: Formal methods for computational systems biology, SFM 2008, Bertinoro, Italy, June 2008. Lecture notes in computer science, vol 5016. Springer, pp 313\u2013365","DOI":"10.1007\/978-3-540-68894-5_9"},{"issue":"7","key":"54_CR005419","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1145\/1272516.1272529","volume":"50","author":"P Denning","year":"2007","unstructured":"Denning P (2007) Computing is a natural science. Commun ACM 50(7):13\u201318","journal-title":"Commun ACM"},{"issue":"24","key":"54_CR005420","doi-asserted-by":"publisher","first-page":"3075","DOI":"10.1093\/bioinformatics\/btl516","volume":"22","author":"C Eccher","year":"2006","unstructured":"Eccher C, Priami C (2006) Design and implementation of a tool for translating sbml into the biochemical stochastic \u03c0-calculus. Bioinformatics 22(24): 3075\u20133081","journal-title":"Bioinformatics"},{"issue":"3","key":"54_CR005421","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1016\/j.csda.2007.05.019","volume":"52","author":"A Golightly","year":"2008","unstructured":"Golightly A, Wilkinson DJ (2008) Bayesian inference for nonlinear multivariate diffusion models observed with error. Comput Stat Data anal 52(3):1674\u20131693","journal-title":"Comput Stat Data anal"},{"key":"54_CR005422","volume-title":"Algorithmic bioprocesses","author":"M Guerriero","year":"2008","unstructured":"Guerriero M, Prandi D, Priami C, Quaglia P (2008) Process calculi abstractions for biology. In: Condon A, Harel D, Kok J, Salomaa A, Winfree E (eds) Algorithmic bioprocesses. Springer, Berlin"},{"key":"54_CR005423","doi-asserted-by":"publisher","first-page":"vii","DOI":"10.1016\/0167-2789(90)90168-O","volume":"45","author":"H Gutowitz","year":"1990","unstructured":"Gutowitz H (1990) Introduction (to cellular automata). Physica D 45:vii","journal-title":"Physica D"},{"key":"54_CR005424","volume-title":"Statecharts in the making: a personal account","author":"D Harel","year":"2007","unstructured":"Harel D (2007) Statecharts in the making: a personal account. In: Proceedings of 3rd ACM SIGPLAN history of programming languages conference (HOPL III), San Diego, CA, June 2007"},{"key":"54_CR005425","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1038\/nature01410","volume":"421","author":"L Hood","year":"2003","unstructured":"Hood L, Galas D (2003) The digital code of DNA. Nature 421:444\u2013448","journal-title":"Nature"},{"key":"54_CR005426","doi-asserted-by":"publisher","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","volume":"22","author":"S Hoops","year":"2006","unstructured":"Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, et al. (2006) COPASI \u2013 a COmplex PAthway SImulator. Bioinformatics 22:3067\u20133074","journal-title":"Bioinformatics"},{"key":"54_CR005427","doi-asserted-by":"publisher","first-page":"1662","DOI":"10.1126\/science.1069492","volume":"295","author":"H Kitano","year":"2002","unstructured":"Kitano H (2002) Systems biology: a brief overview. Science 295:1662\u20131664","journal-title":"Science"},{"issue":"16","key":"54_CR005428","doi-asserted-by":"publisher","first-page":"165101","DOI":"10.1063\/1.2987701","volume":"129","author":"H Kuwahara","year":"2008","unstructured":"Kuwahara H, Mura I (2008) An efficient and exact stochastic simulation method to analyze rare events in biochemical systems. J Chem Phys 129(16):165101","journal-title":"J Chem Phys"},{"key":"54_CR005429","volume-title":"Modeling and simulating reaction-diffusion systems with state-dependent diffusion coefficients","author":"P Lecca","year":"2008","unstructured":"Lecca P, Dematt\u00e9 L, Priami C (2008) Modeling and simulating reaction-diffusion systems with state-dependent diffusion coefficients. In: Proceedings of world academy of science, engineering and technology \u2013 international conference on bioinformatics and biomedicine, vol 35"},{"key":"54_CR005430","volume-title":"A new probabilistic generative model of parameter inference in biochemical networks","author":"P Lecca","year":"2009","unstructured":"Lecca P, Palmisano A, Priami C, Sanguinetti G (2009) A new probabilistic generative model of parameter inference in biochemical networks. In: Proceedings of the 2009 ACM Symposium on Applied Computing, Honolulu, HI, March 2009"},{"key":"54_CR005451","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1752-0509-4-1","volume":"4","author":"T Mazza","year":"2010","unstructured":"Mazza T, Iaccarino G, Priami C (2010) Snazer: the simulations and networks analyzer. BMC Syst Biol 4:1","journal-title":"BMC Systems Biology"},{"key":"54_CR005431","doi-asserted-by":"publisher","first-page":"2467","DOI":"10.1101\/gr.1262503","volume":"13","author":"GC Moles","year":"2003","unstructured":"Moles GC, Mendes P, Banga JR (2003) Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res 13:2467\u20132474","journal-title":"Genome Res."},{"key":"54_CR005432","volume-title":"From ODEs to language-based, executable models of biological systems","author":"I Mura","year":"2009","unstructured":"Mura I, Palmisano A, Priami C (2009) From ODEs to language-based, executable models of biological systems. In: PSB09: Proceedings of the Pacific symposium on biocomputing, Kohala Coast, HI, January 2009"},{"key":"54_CR005433","series-title":"Lecture notes in computer science","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1007\/978-3-540-75140-3_13","volume-title":"Efficient, correct simulation of biological processes in stochastic pi-calculus","author":"A Phillips","year":"2007","unstructured":"Phillips A, Cardelli L (2007) Efficient, correct simulation of biological processes in stochastic pi-calculus. In: Proceedings of CMSB07, Edinburgh, Scotland, September 2007. Lecture notes in computer science, vol 4695. Springer, pp 184\u2013199"},{"issue":"4","key":"54_CR005434","first-page":"1","volume":"3","author":"PK Polisetty","year":"2006","unstructured":"Polisetty PK, Voit EO, Gatzke EP (2006) Identification of metabolic system parameters using global optimization methods. Theor Biol Med Model 3(4):1\u201315","journal-title":"Theor Biol Med Model"},{"issue":"6","key":"54_CR005435","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1093\/comjnl\/38.7.578","volume":"38","author":"C Priami","year":"1995","unstructured":"Priami C (1995) Stochastic \u03c0-calclus. Comput J 38(6):578\u2013589","journal-title":"Comput J"},{"issue":"5","key":"54_CR005436","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1145\/1506409.1506427","volume":"52","author":"C Priami","year":"2009","unstructured":"Priami C (2009) Algorithmic systems biology. Communications of the ACM 52(5):80\u201388","journal-title":"Communication of the ACM"},{"key":"54_CR005437","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1093\/bib\/5.3.259","volume":"5","author":"C Priami","year":"2004","unstructured":"Priami C, Quaglia P (2004) Modeling the dynamics of biosystems. Brief Bioinform 5:259\u2013269","journal-title":"Brief Bioinform"},{"key":"54_CR005438","series-title":"Lecture notes in bioinformatics","first-page":"21","volume-title":"Beta binders for biological interactions","author":"C Priami","year":"2005","unstructured":"Priami C, Quaglia P (2005) Beta binders for biological interactions. In: Proceedings of CMSB04, Paris, France, May 2004. Lecture notes in bioinformatics, vol 3082. Springer, pp 21\u201334"},{"key":"54_CR005439","doi-asserted-by":"publisher","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, Silvermann W (2001) Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Inform Process Lett 80:25\u201331","journal-title":"Inform Process Lett"},{"key":"54_CR005441","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1038\/419343a","volume":"419","author":"A Regev","year":"2003","unstructured":"Regev A, Shapiro E (2003) Cells as computation. Nature 419:343","journal-title":"Nature"},{"issue":"1","key":"54_CR005440","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/j.tcs.2004.03.061","volume":"325","author":"A Regev","year":"2004","unstructured":"Regev A, Panina EM, Silverman W, Cardelli L, Shapiro E (2004) BioAmbients: an abstraction for biological compartments. TCS 325(1):141\u2013167","journal-title":"TCS"},{"key":"54_CR005442","doi-asserted-by":"publisher","first-page":"1260","DOI":"10.1126\/science.291.5507.1260","volume":"291","author":"D Roos","year":"2001","unstructured":"Roos D (2001) Bioinformatics \u2013 trying to swim in a sea of data. Science 291:1260\u20131261","journal-title":"Science"},{"key":"54_CR005443","volume-title":"Essays on life itself","author":"R Rosen","year":"1998","unstructured":"Rosen R (1998) Essays on life itself. Columbia University Press, New York"},{"key":"54_CR005444","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1038\/nature01255","volume":"420","author":"D Searls","year":"2002","unstructured":"Searls D (2002) The language of genes. Nature 420:211\u2013217","journal-title":"Nature"},{"issue":"20","key":"54_CR005445","doi-asserted-by":"publisher","first-page":"2800","DOI":"10.1093\/bioinformatics\/btm416","volume":"23","author":"S Sedwards","year":"2007","unstructured":"Sedwards S, Mazza T (2007) Cyto-sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes. Bioinformatics 23(20):2800\u20132802","journal-title":"Bioinformatics"},{"key":"54_CR005446","doi-asserted-by":"publisher","first-page":"1221","DOI":"10.1126\/science.287.5456.1221","volume":"287","author":"S Spengler","year":"2000","unstructured":"Spengler S (2000) Bioinformatics in the information age. Science 287:1221\u20131223","journal-title":"Science"},{"key":"54_CR005447","unstructured":"The Kappa Factory. \n                  http:\/\/www.lix.polytechnique.fr\/~krivine\/kappaFactory.html"},{"issue":"1","key":"54_CR005448","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1093\/bioinformatics\/btl552","volume":"23","author":"T Tian","year":"2007","unstructured":"Tian T, Xu S, Burrage K (2007) Simulated maximum likelihood method for estimating kinetic rates in gene expression. Bioinformatics 23(1):84\u201391","journal-title":"Bioinformatics"},{"key":"54_CR005449","series-title":"Lecture notes in computer science","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1007\/11423348_10","volume-title":"Communicating mobile processes: introducing occam-pi","author":"P Welch","year":"2005","unstructured":"Welch P, Barnes F (2005) Communicating mobile processes: introducing occam-pi. In: Proceedings of CSP25, London, July 2004. Lecture notes in computer science, vol 3525. Springer, pp 175\u2013210"},{"issue":"3","key":"54_CR005450","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1145\/1118178.1118215","volume":"49","author":"J Wing","year":"2006","unstructured":"Wing J (2006) Computational thinking. Commun ACM 49(3):33\u201335","journal-title":"Commun ACM"}],"container-title":["Handbook of Natural Computing"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-92910-9_54.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,4,27]],"date-time":"2021-04-27T08:17:12Z","timestamp":1619511432000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-92910-9_54"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012]]},"ISBN":["9783540929093","9783540929109"],"references-count":50,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-92910-9_54","relation":{},"subject":[],"published":{"date-parts":[[2012]]}}}