{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,5]],"date-time":"2024-09-05T05:39:13Z","timestamp":1725514753702},"publisher-location":"Berlin, Heidelberg","reference-count":32,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540688921"},{"type":"electronic","value":"9783540688945"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008]]},"DOI":"10.1007\/978-3-540-68894-5_10","type":"book-chapter","created":{"date-parts":[[2008,5,30]],"date-time":"2008-05-30T12:39:25Z","timestamp":1212151165000},"page":"366-386","source":"Crossref","is-referenced-by-count":2,"title":["Cells in Silico: A Holistic Approach"],"prefix":"10.1007","author":[{"given":"Davide","family":"Chiarugi","sequence":"first","affiliation":[]},{"given":"Pierpaolo","family":"Degano","sequence":"additional","affiliation":[]},{"given":"Jan Bert","family":"Van Klinken","sequence":"additional","affiliation":[]},{"given":"Roberto","family":"Marangoni","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"key":"10_CR1","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1006\/abio.2001.5183","volume":"295","author":"A. Buchholz","year":"2001","unstructured":"Buchholz, A., Takors, R., Wandrey, C.: Quantification of intracellular metabolites in escherichia coli k12 using liquid chromatographic-electrospray ionization tandem mass spectrometric techniques. Analytical Biochemistry\u00a0295, 129\u2013137 (2001)","journal-title":"Analytical Biochemistry"},{"key":"10_CR2","unstructured":"Cardelli, L.: From processes to odes by chemistry, draft (2006)"},{"key":"10_CR3","unstructured":"Cardelli, L., Phillips, A.: A correct abstract machine for stochastic pi-calculus. In: Procs. BioConcur (2004)"},{"key":"10_CR4","series-title":"Lecture Notes in Bioinformatics","volume-title":"Computational Methods in Systems Biology","author":"D. Chiarugi","year":"2005","unstructured":"Chiarugi, D., Curti, M., Degano, P., Marangoni, R.: ViCe: a VIrtual CEll. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol.\u00a03082, Springer, Heidelberg (2005)"},{"key":"10_CR5","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","DOI":"10.1007\/3-540-36481-1_3","volume-title":"Computational Methods in Systems Biology","author":"M. Curti","year":"2003","unstructured":"Curti, M., Degano, P., Baldari, C.T.: Causal \u03c0-calculus for biochemical modelling. In: Priami, C. (ed.) CMSB 2003. LNCS, vol.\u00a02602, Springer, Heidelberg (2003)"},{"key":"10_CR6","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.tcs.2004.03.066","volume":"325","author":"M. Curti","year":"2004","unstructured":"Curti, M., Degano, P., Priami, C., Baldari, C.T.: Modelling biochemical pathways through enhanced \u03c0-calculus. Theoretical Computer Science\u00a0325\/1, 111\u2013140 (2004)","journal-title":"Theoretical Computer Science"},{"issue":"2","key":"10_CR7","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1145\/234528.234748","volume":"28","author":"P. Degano","year":"1996","unstructured":"Degano, P., Priami, C.: Enhanced operational semantics. ACM Computing Surveys\u00a028(2), 352\u2013354 (1996)","journal-title":"ACM Computing Surveys"},{"issue":"1","key":"10_CR8","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1006\/bbrc.2000.2603","volume":"271","author":"J.C. Diaz Ricci","year":"2000","unstructured":"Diaz Ricci, J.C.: Adp modulates the dynamic behavior of the glycolytic pathway of Escherichia coli. Biochemical and Biophysical Research Communications\u00a0271(1), 244\u2013249 (2000)","journal-title":"Biochemical and Biophysical Research Communications"},{"key":"10_CR9","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1046\/j.1462-2920.2002.00282.x","volume":"4","author":"J.S. Edwards","year":"2002","unstructured":"Edwards, J.S., Cover, M., Palsson, B.O.: Metabolic modelling of microbes: the flux-balance approach. Env. Microbiol.\u00a04, 133\u2013140 (2002)","journal-title":"Env. Microbiol."},{"key":"10_CR10","first-page":"125","volume":"19","author":"J.S. Edwards","year":"2001","unstructured":"Edwards, J.S., Ibarra, R.U., Palsson, B.O.: In silico predictions of escherichia coli metabolic capabilities are consistent with experimental data. predictions of escherichia coli metabolic capabilities are consistent with experimental data\u00a019, 125\u2013130 (2001)","journal-title":"predictions of escherichia coli metabolic capabilities are consistent with experimental data"},{"key":"10_CR11","doi-asserted-by":"publisher","first-page":"5528","DOI":"10.1073\/pnas.97.10.5528","volume":"97","author":"J.S. Edwards","year":"2000","unstructured":"Edwards, J.S., Palsson, B.O.: The escherichia coli mg1655 in silico metabolic genotype: its definition, characteristics and capabilities. Proc. Natl. Acad. Sci. USA\u00a097, 5528\u20135533 (2000)","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10_CR12","doi-asserted-by":"crossref","DOI":"10.1002\/0471254959","volume-title":"Textbook of Biochemistry","author":"T.M. Devlin","year":"2002","unstructured":"Devlin, T.M., et al.: Textbook of Biochemistry, 5th edn. Wiley and Sons, Inc, Chichester (2002)","edition":"5"},{"key":"10_CR13","volume-title":"Understanding the control of metabolism","author":"D.A. Fell","year":"1997","unstructured":"Fell, D.A.: Understanding the control of metabolism. Portland Press, London, United Kingdom (1997)"},{"key":"10_CR14","volume-title":"Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding","author":"A. Fersht","year":"1999","unstructured":"Fersht, A.: Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. Freeman, New York (1999)"},{"key":"10_CR15","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1007\/BF01020385","volume":"3","author":"D.T. Gillespie","year":"1977","unstructured":"Gillespie, D.T.: Concerning the validity of the stochastic approach to chemical kinetics. Journal of Statistical Physics\u00a03, 311\u2013318 (1977)","journal-title":"Journal of Statistical Physics"},{"issue":"25","key":"10_CR16","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"},{"key":"10_CR17","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1146\/annurev.physchem.58.032806.104637","volume":"58","author":"D.T. Gillespie","year":"2007","unstructured":"Gillespie, D.T.: Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem.\u00a058, 35\u201355 (2007)","journal-title":"Annu. Rev. Phys. Chem."},{"key":"10_CR18","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1073\/pnas.0510013103","volume":"103","author":"J. Glass","year":"2006","unstructured":"Glass, J., Assad-Garcia, N., Alperovich, N.: Essential genes of a minimal bacterium. PNAS\u00a0103, 425\u2013430 (2006)","journal-title":"PNAS"},{"key":"10_CR19","doi-asserted-by":"publisher","first-page":"1844","DOI":"10.1128\/AEM.66.5.1844-1850.2000","volume":"66","author":"R.R. Gokarn","year":"2000","unstructured":"Gokarn, R.R., Eiteman, M.A., Altman, A.: Metabolic analysis of escherichia coli in the presence and absence of the carboxylating enzymes phosphoenolpyruvate carboxylase and pyruvate carboxylase. App. Env. Microbiol.\u00a066, 1844\u20131850 (2000)","journal-title":"App. Env. Microbiol."},{"key":"10_CR20","volume-title":"The Enzymes","author":"G.G. Hammes","year":"1970","unstructured":"Hammes, G.G., Shimmel, P.R.: The Enzymes, P.D. Boyer, vol.\u00a02. New York Academic Press, London (1970)"},{"key":"10_CR21","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1529\/biophysj.106.093138","volume":"92","author":"C.S. Henry","year":"2007","unstructured":"Henry, C.S., Broadbelt, L.J., Hatzimanikatis, V.: Thermodynamics-based metabolic flux analysis. Biophys. J.\u00a092, 1792\u20131805 (2007)","journal-title":"Biophys. J."},{"key":"10_CR22","doi-asserted-by":"publisher","first-page":"989","DOI":"10.1073\/pnas.51.6.989","volume":"51","author":"J. Higgins","year":"1964","unstructured":"Higgins, J.: A chemical mechanism for oscillation of glycolytic intermediates in yeast cell. Proceeding of National Academy Science USA\u00a051, 989\u2013994 (1964)","journal-title":"Proceeding of National Academy Science USA"},{"key":"10_CR23","doi-asserted-by":"publisher","first-page":"7053","DOI":"10.1128\/JB.185.24.7053-7067.2003","volume":"185","author":"Q. Hua","year":"2003","unstructured":"Hua, Q., Yang, C., Baba, T., Mori, H., Shimizu, K.: Responses of the central metabolism in escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts. J. Bacteriol.\u00a0185, 7053\u20137067 (2003)","journal-title":"J. Bacteriol."},{"key":"10_CR24","volume-title":"Foundations of System Biology","author":"H. Kitano","year":"2002","unstructured":"Kitano, H.: Foundations of System Biology. MIT Press, Cambridge (2002)"},{"key":"10_CR25","doi-asserted-by":"publisher","first-page":"10268","DOI":"10.1073\/pnas.93.19.10268","volume":"93","author":"A.R. Mushegian","year":"1996","unstructured":"Mushegian, A.R., Koonin, E.V.: A minimal gene set fir cellular life derived by comparison of complete bacterial genome. Proceedings of National Academy of Science USA\u00a093, 10268\u201310273 (1996)","journal-title":"Proceedings of National Academy of Science USA"},{"key":"10_CR26","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1109\/32.962559","volume":"10","author":"C. Nottegar","year":"2001","unstructured":"Nottegar, C., Priami, C., Degano, P.: Performance evaluation of mobile processes via abstract machines. IEEE Transactions on Software Engineering\u00a010, 867\u2013889 (2001)","journal-title":"IEEE Transactions on Software Engineering"},{"issue":"6","key":"10_CR27","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":"10_CR28","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., Silverman, W., Shapiro, E.: Application of a stochastic passing-name calculus to representation and simulation of molecular processes. Information Processing Letters\u00a080, 25\u201331 (2001)","journal-title":"Information Processing Letters"},{"key":"10_CR29","doi-asserted-by":"publisher","first-page":"2692","DOI":"10.1128\/JB.185.9.2692-2699.2003","volume":"185","author":"J.L. Reed","year":"2003","unstructured":"Reed, J.L., Palsson, B.O.: Thirteen years of building constraint-based in silico models of escherichia coli. J. Bacteriol.\u00a0185, 2692\u20132699 (2003)","journal-title":"J. Bacteriol."},{"issue":"54","key":"10_CR30","first-page":"1","volume":"4","author":"J.L. Reed","year":"2000","unstructured":"Reed, J.L., Vo, T.D., Schilling, C.H., Palsson, B.O.: An expanded genome-scale model of escherichia coli k-12 (ijr904 gsm\/gpr). Genome Biol\u00a0R54.1\u2013R54.12 (2000)","journal-title":"Genome Biol"},{"key":"10_CR31","doi-asserted-by":"crossref","unstructured":"Regev, A., Silverman, W., Shapiro, E.: Representation and simulation of biochemical processes using the \u03c0-calculus process algebra. In: Pacific Symposium of Biocomputing (PSB 2001), pp. 459\u2013470 (2001)","DOI":"10.1142\/9789814447362_0045"},{"key":"10_CR32","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1016\/j.jtbi.2005.11.024","volume":"241","author":"O.S. Soyer","year":"2006","unstructured":"Soyer, O.S., Pfeiffer, T., Bonhoeffer, S.: Simulating the evolution of signal transduction pathways. Journal of theoretical biology\u00a0241, 223\u2013232 (2006)","journal-title":"Journal of theoretical biology"}],"container-title":["Lecture Notes in Computer Science","Formal Methods for Computational Systems Biology"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-68894-5_10","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,11]],"date-time":"2019-05-11T20:08:34Z","timestamp":1557605314000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-68894-5_10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008]]},"ISBN":["9783540688921","9783540688945"],"references-count":32,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-68894-5_10","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2008]]}}}