{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T01:35:09Z","timestamp":1790818509535,"version":"4.1.0"},"publisher-location":"Berlin, Heidelberg","reference-count":26,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"value":"9783540253754","type":"print"},{"value":"9783540259749","type":"electronic"}],"license":[{"start":{"date-parts":[[2005,1,1]],"date-time":"2005-01-01T00:00:00Z","timestamp":1104537600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005]]},"DOI":"10.1007\/978-3-540-25974-9_14","type":"book-chapter","created":{"date-parts":[[2010,2,25]],"date-time":"2010-02-25T19:23:04Z","timestamp":1267125784000},"page":"172-191","source":"Crossref","is-referenced-by-count":37,"title":["The Biochemical Abstract Machine BIOCHAM"],"prefix":"10.1007","author":[{"given":"Nathalie","family":"Chabrier-Rivier","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fran\u00e7ois","family":"Fages","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylvain","family":"Soliman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","reference":[{"key":"14_CR1","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1146\/annurev.genom.2.1.343","volume":"2","author":"T. Ideker","year":"2001","unstructured":"Ideker, T., Galitski, T., Hood, L.: A new approach to decoding life: Systems biology. Annual Review of Genomics and Human Genetics\u00a02, 343\u2013372 (2001)","journal-title":"Annual Review of Genomics and Human Genetics"},{"key":"14_CR2","doi-asserted-by":"crossref","unstructured":"Regev, A., Silverman, W., Shapiro, E.Y.: Representation and simulation of biochemical processes using the pi-calculus process algebra. In: Proceedings of the sixth Pacific Symposium of Biocomputing, pp. 459\u2013470 (2001)","DOI":"10.1142\/9789814447362_0045"},{"key":"14_CR3","unstructured":"Nagasaki, M., Onami, S., Miyano, S., Kitano, H.: Bio-calculus: Its concept, and an application for molecular interaction. In: Currents in Computational Molecular Biology. Frontiers Science Series, vol.\u00a030, Universal Academy Press, Inc. (2000) (This book is a collection of poster papers presented at the RECOMB 2000, Poster Session)"},{"key":"14_CR4","doi-asserted-by":"crossref","unstructured":"Eker, S., Knapp, M., Laderoute, K., Lincoln, P., Meseguer, J., S\u00f6nmez, M.K.: Pathway logic: Symbolic analysis of biological signaling. In: Proceedings of the seventh Pacific Symposium on Biocomputing, pp. 400\u2013412 (2002)","DOI":"10.1142\/9789812799623_0038"},{"key":"14_CR5","unstructured":"Matsuno, H., Doi, A., Nagasaki, M., Miyano, S.: Hybrid petri net representation of gene regulatory network. In: Proceedings of the 5th Pacific Symposium on Biocomputing, pp. 338\u2013349 (2000)"},{"key":"14_CR6","first-page":"39","volume-title":"Silico Biology","author":"R. Hofest\u00e4dt","year":"1998","unstructured":"Hofest\u00e4dt, R., Thelen, S.: Quantitative modeling of biochemical networks. In: Silico Biology, vol.\u00a01, pp. 39\u201353. IOS Press, Amsterdam (1998)"},{"key":"14_CR7","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1007\/3-540-45351-2_6","volume-title":"Hybrid Systems: Computation and Control","author":"R. Alur","year":"2001","unstructured":"Alur, R., Belta, C., Ivan\u010di\u0107, F., Kumar, V., Mintz, M., Pappas, G.J., Rubin, H., Schug, J.: Hybrid modeling and simulation of biomolecular networks. In: Di Benedetto, M.D., Sangiovanni-Vincentelli, A.L. (eds.) HSCC 2001. LNCS, vol.\u00a02034, pp. 19\u201332. Springer, Heidelberg (2001)"},{"key":"14_CR8","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1007\/3-540-45351-2_21","volume-title":"Hybrid Systems: Computation and Control","author":"R. Ghosh","year":"2001","unstructured":"Ghosh, R., Tomlin, C.J.: Lateral inhibition through delta-notch signaling: A piecewise affine hybrid model. In: Di Benedetto, M.D., Sangiovanni-Vincentelli, A.L. (eds.) HSCC 2001. LNCS, vol.\u00a02034, pp. 232\u2013246. Springer, Heidelberg (2001)"},{"key":"14_CR9","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1007\/3-540-45619-8_7","volume-title":"Logic Programming","author":"A. Bockmayr","year":"2002","unstructured":"Bockmayr, A., Courtois, A.: Using hybrid concurrent constraint programming to model dynamic biological systems. In: Stuckey, P.J. (ed.) ICLP 2002. LNCS, vol.\u00a02401, pp. 85\u201399. Springer, Heidelberg (2002)"},{"key":"14_CR10","unstructured":"ARC CPBIO: Process calculi and biology of molecular networks (2002\u20132003), http:\/\/contraintes.inria.fr\/cpbio\/"},{"key":"14_CR11","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1007\/3-540-45657-0_29","volume-title":"Computer Aided Verification","author":"A. Cimatti","year":"2002","unstructured":"Cimatti, A., Clarke, E., Giunchiglia, E., Giunchiglia, F., Pistore, M., Roveri, M., Sebastiani, R., Tacchella, A.: NuSMV 2: An openSource tool for symbolic model checking. In: Brinksma, E., Larsen, K.G. (eds.) CAV 2002. LNCS, vol.\u00a02404, p. 359. Springer, Heidelberg (2002)"},{"key":"14_CR12","volume-title":"Model Checking","author":"E.M. Clarke","year":"1999","unstructured":"Clarke, E.M., Grumberg, O., Peled, D.A.: Model Checking. MIT Press, Cambridge (1999)"},{"key":"14_CR13","doi-asserted-by":"crossref","unstructured":"Chabrier, N., Chiaverini, M., Danos, V., Fages, F., Sch\u00e4chter, V.: Modeling and querying biochemical networks. In: Theoretical Computer Science (to appear, 2004)","DOI":"10.1016\/j.tcs.2004.03.063"},{"key":"14_CR14","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1007\/3-540-36481-1_13","volume-title":"Computational Methods in Systems Biology","author":"N. Chabrier","year":"2003","unstructured":"Chabrier, N., Fages, F.: Symbolic model checking of biochemical networks. In: Priami, C. (ed.) CMSB 2003. LNCS, vol.\u00a02602, pp. 149\u2013162. Springer, Heidelberg (2003)"},{"key":"14_CR15","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1007\/3-540-36481-1_16","volume-title":"Computational Methods in Systems Biology","author":"M. Chiaverini","year":"2003","unstructured":"Chiaverini, M., Danos, V.: A core modeling language for the working molecular biologist (Abstract). In: Priami, C. (ed.) CMSB 2003. LNCS, vol.\u00a02602, pp. 166\u2013166. Springer, Heidelberg (2003)"},{"key":"14_CR16","doi-asserted-by":"publisher","first-page":"2703","DOI":"10.1091\/mbc.10.8.2703","volume":"10","author":"K.W. Kohn","year":"1999","unstructured":"Kohn, K.W.: Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Molecular Biology of Cell\u00a010, 2703\u20132734 (1999)","journal-title":"Molecular Biology of Cell"},{"key":"14_CR17","unstructured":"Maimon, R., Browning, S.: Diagrammatic notation and computational structure of gene networks. In: Yi, T.M., Hucka, M., Morohashi, M., Kitano, H. (eds.) Proceedings of the 2nd International Conference on Systems Biology, Online Proceedings (2001), http:\/\/www.icsb2001.org\/toc.html"},{"key":"14_CR18","volume-title":"Expert Reviews in Molecular Medicine","author":"W. Kolch","year":"2002","unstructured":"Kolch, W., Kotwaliwale, A., Vass, K., Janosch, P.: The role of raf kinases in malignant transformation. In: Expert Reviews in Molecular Medicine, vol.\u00a025. Cambridge University Press, Cambridge (2002), http:\/\/www.expertreviews.org\/02004386h.htm"},{"key":"14_CR19","doi-asserted-by":"publisher","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, B.J., Mjolsness, E.D.: Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinformatics\u00a019, 677\u2013678 (2003), http:\/\/www-aig.jpl.nasa.gov\/public\/mls\/cellerator\/","journal-title":"Bioinformatics"},{"key":"14_CR20","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\u00a019, 524\u2013531 (2003), http:\/\/sbml.org","journal-title":"Bioinformatics"},{"key":"14_CR21","doi-asserted-by":"publisher","first-page":"5818","DOI":"10.1073\/pnas.97.11.5818","volume":"97","author":"A. Levchenko","year":"2000","unstructured":"Levchenko, A., Bruck, J., Sternberg, P.W.: Scaffold proteins biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. PNAS\u00a097, 5818\u20135823 (2000)","journal-title":"PNAS"},{"key":"14_CR22","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M. Kanehisa","year":"2000","unstructured":"Kanehisa, M., Goto, S.: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research\u00a028, 27\u201330 (2000)","journal-title":"Nucleic Acids Research"},{"key":"14_CR23","series-title":"Lecture Notes in Bioinformatics","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1007\/978-3-540-25974-9_19","volume-title":"Computational Methods in Systems Biology","author":"S. Soliman","year":"2005","unstructured":"Soliman, S., Fages, F.: CMBSlib: A library for comparing formalisms and models of biological systems. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol.\u00a03082, pp. 231\u2013235. Springer, Heidelberg (2005)"},{"key":"14_CR24","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1007\/BF03037227","volume":"13","author":"S.H. Muggleton","year":"1995","unstructured":"Muggleton, S.H.: Inverse entailment and progol. New Generation Computing\u00a013, 245\u2013286 (1995)","journal-title":"New Generation Computing"},{"key":"14_CR25","doi-asserted-by":"crossref","unstructured":"Schaff, J., Loew, L.M.: The virtual cell. In: Proceedings of the fourth Pacific Symposium on Biocomputing, pp. 228\u2013239 (1999)","DOI":"10.1142\/9789814447300_0023"},{"key":"14_CR26","first-page":"391","volume":"11","author":"K.C. Chen","year":"2000","unstructured":"Chen, K.C., Csik\u00e1sz-Nagy, A., Gy\u00f6rffy, B., Val, J., Nov\u00e0k, B., Tyson, J.J.: Kinetic analysis of a molecular model of the budding yeast cell cycle. Molecular Biology of the Cell\u00a011, 391\u2013396 (2000)","journal-title":"Molecular Biology of the Cell"}],"container-title":["Lecture Notes in Computer Science","Computational Methods in Systems Biology"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-25974-9_14","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,18]],"date-time":"2025-02-18T21:58:25Z","timestamp":1739915905000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-25974-9_14"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005]]},"ISBN":["9783540253754","9783540259749"],"references-count":26,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-25974-9_14","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005]]}}}