{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T18:12:22Z","timestamp":1743012742321,"version":"3.40.3"},"publisher-location":"Berlin, Heidelberg","reference-count":36,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642117114"},{"type":"electronic","value":"9783642117121"}],"license":[{"start":{"date-parts":[[2010,1,1]],"date-time":"2010-01-01T00:00:00Z","timestamp":1262304000000},"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":[[2010]]},"DOI":"10.1007\/978-3-642-11712-1_5","type":"book-chapter","created":{"date-parts":[[2010,2,11]],"date-time":"2010-02-11T20:48:43Z","timestamp":1265921323000},"page":"163-198","source":"Crossref","is-referenced-by-count":1,"title":["Modelling Self-assembly in BlenX"],"prefix":"10.1007","author":[{"given":"Roberto","family":"Larcher","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Corrado","family":"Priami","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandro","family":"Romanel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"5_CR1","unstructured":"http:\/\/www.cosbi.eu\/downloads\/attachment\/Models.tar.gz"},{"key":"5_CR2","unstructured":"Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P.: Molecular biology of the cell (IV ed.). Garland science (2002)"},{"issue":"3","key":"5_CR3","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1016\/j.tcs.2007.11.012","volume":"391","author":"L. Cardelli","year":"2008","unstructured":"Cardelli, L.: On process rate semantics. Theor. Comput. Sci.\u00a0391(3), 190\u2013215 (2008)","journal-title":"Theor. Comput. Sci."},{"issue":"1","key":"5_CR4","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1016\/j.entcs.2009.02.009","volume":"229","author":"L. Cardelli","year":"2009","unstructured":"Cardelli, L., Caron, E., Gardner, P., Kahramano\u011fullar\u0131, O., Phillips, A.: A Process Model of Actin Polymerisation. Electronic Notes in Theoretical Computer Science\u00a0229(1), 127\u2013144 (2009)","journal-title":"Electronic Notes in Theoretical Computer Science"},{"issue":"2","key":"5_CR5","doi-asserted-by":"publisher","first-page":"1074","DOI":"10.1016\/S0006-3495(04)74182-X","volume":"86","author":"A.E. Carlsson","year":"2004","unstructured":"Carlsson, A.E., Wear, M.A., Cooper, J.A.: End versus side branching by Arp2\/3 complex. Biophysical journal\u00a086(2), 1074\u20131081 (2004)","journal-title":"Biophysical journal"},{"issue":"1-2","key":"5_CR6","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/j.tcs.2008.04.014","volume":"404","author":"P. Curien","year":"2008","unstructured":"Curien, P., Danos, V., Krivine, J., Zhang, M.: Computational self-assembly. Theor. Comput. Sci.\u00a0404(1-2), 61\u201375 (2008)","journal-title":"Theor. Comput. Sci."},{"key":"5_CR7","doi-asserted-by":"crossref","unstructured":"Danos, V., Feret, J., Fontana, W., Harmer, R., Krivine, J.: Rule-based modelling of cellular signalling. In: CONCUR, pp. 17\u201341 (2007)","DOI":"10.1007\/978-3-540-74407-8_3"},{"key":"5_CR8","unstructured":"Dematt\u00e9, L., Larcher, R.: Custom visualization of biological structures: an application to BlenX complexes. Technical Report TR-16-2009 CoSBi (2009)"},{"issue":"5","key":"5_CR9","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.: The Beta Workbench: a computational tool to study the dynamics of biological systems. Brief. Bioinform.\u00a09(5), 437\u2013449 (2008)","journal-title":"Brief. Bioinform."},{"key":"5_CR10","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1007\/978-3-540-68894-5_9","volume-title":"Formal Methods for Computational Systems Biology","author":"L. Dematt\u00e9","year":"2008","unstructured":"Dematt\u00e9, L., Priami, C., Romanel, A.: The BlenX Language: A Tutorial. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol.\u00a05016, pp. 313\u2013365. Springer, Heidelberg (2008)"},{"key":"5_CR11","volume-title":"Nanosystems: molecular machinery, manufacturing, and computation","author":"E.K. Drexler","year":"1992","unstructured":"Drexler, E.K.: Nanosystems: molecular machinery, manufacturing, and computation. Wiley, Chichester (1992)"},{"issue":"1","key":"5_CR12","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/j.jtbi.2008.01.001","volume":"252","author":"J. Fass","year":"2008","unstructured":"Fass, J., Pak, C., Bamburg, J., Mogilner, A.: Stochastic simulation of actin dynamics reveals the role of annealing and fragmentation. Journal of theoretical biology\u00a0252(1), 173\u2013183 (2008)","journal-title":"Journal of theoretical biology"},{"issue":"3","key":"5_CR13","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1089\/106652700750050961","volume":"7","author":"N. Friedman","year":"2000","unstructured":"Friedman, N., Linial, M., Nachman, I., Pe\u2019er, D.: Using Bayesian networks to analyze expression data. Journal of Computational Biology\u00a07(3), 601\u2013620 (2000)","journal-title":"Journal of Computational Biology"},{"issue":"25","key":"5_CR14","doi-asserted-by":"publisher","first-page":"2340","DOI":"10.1021\/j100540a008","volume":"81","author":"D.T. Gillespie","year":"1977","unstructured":"Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry\u00a081(25), 2340\u20132361 (1977)","journal-title":"Journal of Physical Chemistry"},{"issue":"6912","key":"5_CR15","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1038\/nature01257","volume":"420","author":"J. Hasty","year":"2002","unstructured":"Hasty, J., McMillen, D., Collins, J.J.: Engineered gene circuits. Nature\u00a0420(6912), 224\u2013230 (2002)","journal-title":"Nature"},{"key":"5_CR16","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1007\/978-3-540-68894-5_7","volume-title":"Formal Methods for Computational Systems Biology","author":"M. Heiner","year":"2008","unstructured":"Heiner, M., Gilbert, D., Donaldson, R.: Petri nets for systems and synthetic biology. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol.\u00a05016, pp. 215\u2013264. Springer, Heidelberg (2008)"},{"issue":"3","key":"5_CR17","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1016\/0022-5193(69)90015-0","volume":"22","author":"S.A. Kauffman","year":"1969","unstructured":"Kauffman, S.A.: Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of theoretical biology\u00a022(3), 437\u2013467 (1969)","journal-title":"Journal of theoretical biology"},{"key":"5_CR18","unstructured":"Klavins, E.: Automatic synthesis of controllers for assembly and formation forming. In: International Conference on Robotics and Automation (2002)"},{"key":"5_CR19","doi-asserted-by":"crossref","unstructured":"Kuttler, C., Lhoussaine, C., Nebut, M.: Rule-based modeling of transcriptional attenuation at the tryptophan operon. In: Formal Methods in Molecular Biology (2009)","DOI":"10.1109\/WSC.2009.5429721"},{"key":"5_CR20","volume-title":"Molecular cell biology","author":"H.F. Lodish","year":"2003","unstructured":"Lodish, H.F.: Molecular cell biology. W.H. Freeman, New York (2003)"},{"issue":"4","key":"5_CR21","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1016\/j.jtbi.2007.08.018","volume":"249","author":"A. Matzavinos","year":"2007","unstructured":"Matzavinos, A., Othmer, H.G.: A stochastic analysis of actin polymerization in the presence of twinfilin and gelsolin. Journal of theoretical biology\u00a0249(4), 723\u2013736 (2007)","journal-title":"Journal of theoretical biology"},{"key":"5_CR22","volume-title":"Communicating and mobile systems: the \u03c0-calculus","author":"R. Milner","year":"1999","unstructured":"Milner, R.: Communicating and mobile systems: the \u03c0-calculus. Cambridge Universtity Press, Cambridge (1999)"},{"issue":"3","key":"5_CR23","doi-asserted-by":"publisher","first-page":"1237","DOI":"10.1016\/S0006-3495(02)73897-6","volume":"83","author":"A. Mogilner","year":"2002","unstructured":"Mogilner, A., Edelstein-Keshet, L.: Regulation of actin dynamics in rapidly moving cells: a quantitative analysis. Biophysical journal\u00a083(3), 1237\u20131258 (2002)","journal-title":"Biophysical journal"},{"key":"5_CR24","doi-asserted-by":"crossref","unstructured":"Nagpal, R.: Programmable self-assembly using biologically-inspired multiagent control. In: AAMAS 2002: Proceedings of the first international joint conference on Autonomous agents and multiagent systems, pp. 418\u2013425 (2002)","DOI":"10.1145\/544741.544839"},{"issue":"3","key":"5_CR25","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1109\/TPAMI.2003.1182095","volume":"25","author":"A. Neumann","year":"2003","unstructured":"Neumann, A.: Graphical gaussian shape models and their application to image segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence\u00a025(3), 316\u2013329 (2003)","journal-title":"IEEE Transactions on Pattern Analysis and Machine Intelligence"},{"issue":"7","key":"5_CR26","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1038\/35017011","volume":"2","author":"D. Pantaloni","year":"2000","unstructured":"Pantaloni, D., Boujemaa, R., Didry, D., Gounon, P., Carlier, M.F.: The Arp2\/3 complex branches filament barbed ends: functional antagonism with capping proteins. Nature cell biology\u00a02(7), 385\u2013391 (2000)","journal-title":"Nature cell biology"},{"key":"5_CR27","series-title":"Lecture Notes in Bioinformatics","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1007\/978-3-540-75140-3_13","volume-title":"Computational Methods in Systems Biology","author":"A. Phillips","year":"2007","unstructured":"Phillips, A., Cardelli, L.: Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus. In: Calder, M., Gilmore, S. (eds.) CMSB 2007. LNCS (LNBI), vol.\u00a04695, pp. 184\u2013199. Springer, Heidelberg (2007)"},{"key":"5_CR28","first-page":"167","volume":"75","author":"D. Prandi","year":"2008","unstructured":"Prandi, D., Priami, C., Quaglia, P.: Communicating by compatibility. JLAP\u00a075, 167 (2008)","journal-title":"JLAP"},{"key":"5_CR29","unstructured":"Prandi, D., Zunino, R.: Computing by Complexes. Technical Report TR-11-2009 CoSBi (2009)"},{"issue":"6","key":"5_CR30","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1093\/comjnl\/38.7.578","volume":"38","author":"C. Priami","year":"1995","unstructured":"Priami, C.: Stochastic \u03c0-calculus. The Computer Journal\u00a038(6), 578\u2013589 (1995)","journal-title":"The Computer Journal"},{"key":"5_CR31","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1007\/978-3-642-04081-8_4","volume-title":"CONCUR 2009","author":"C. Priami","year":"2009","unstructured":"Priami, C., Quaglia, P., Romanel, A.: BlenX Static and Dynamic Semantics. In: Bravetti, M., Zavattaro, G. (eds.) CONCUR 2009. LNCS, vol.\u00a05710, pp. 37\u201352. Springer, Heidelberg (2009)"},{"issue":"1","key":"5_CR32","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.Y., Silverman, W.: Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Inf. Process. Lett.\u00a080(1), 25\u201331 (2001)","journal-title":"Inf. Process. Lett."},{"issue":"1-2","key":"5_CR33","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1016\/j.tcs.2008.04.007","volume":"404","author":"A. Romanel","year":"2008","unstructured":"Romanel, A., Priami, C.: On the decidability and complexity of the structural congruence for beta-binders. Theor. Comput. Sci.\u00a0404(1-2), 156\u2013169 (2008)","journal-title":"Theor. Comput. Sci."},{"key":"5_CR34","volume-title":"The \u03c0-calculus: a Theory of Mobile Processes","author":"D. Sangiorgi","year":"2003","unstructured":"Sangiorgi, D., Walker, D.: The \u03c0-calculus: a Theory of Mobile Processes. Cambridge University Press, Cambridge (2003)"},{"key":"5_CR35","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1146\/annurev.biochem.69.1.183","volume":"69","author":"A.M. Stock","year":"2000","unstructured":"Stock, A.M., Goudreau, P.N., Robinson, V.L.: Two-component signal transduction. Annu. Rev. Biochem.\u00a069, 183\u2013215 (2000)","journal-title":"Annu. Rev. Biochem."},{"key":"5_CR36","doi-asserted-by":"crossref","unstructured":"Yin, P., Choi, H.M.T., Calvert, C.R., Pierce, N.A.: Programming biomolecular self-assembly pathways. Nature\u00a0451(318-322) (2008)","DOI":"10.1038\/nature06451"}],"container-title":["Lecture Notes in Computer Science","Transactions on Computational Systems Biology XII"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-11712-1_5","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,19]],"date-time":"2019-05-19T13:39:31Z","timestamp":1558273171000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-11712-1_5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010]]},"ISBN":["9783642117114","9783642117121"],"references-count":36,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-11712-1_5","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2010]]}}}