Abstract
We report on the specification and analysis of VICE, a hypothetical cell with a genome as basic as possible. We used an enhanced version of the π-calculus and a prototype running it to study the behaviour of VICE. The results of our experimentation in silico confirm that our virtual cell “survives” in an optimal environment and shows a behaviour similar to that of real prokaryotes.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Almaas, E., Kowács, B., et al.: Global organization of metabolic fluxes in the bacterium. Escherichia Coli. Nature 427, 839–843 (2004)
Bodei, C., Buchholtz, M., Degano, P., Curti, M., Priami, C., Nielson, F., Riis Nielson, H.: Performance evaluation of security protocols specified in LySa. In: Procs. of the 2nd W/S on Quantitative Aspects of Programming Languages, ENTCS (2004)
Chiaverini, M., Danos, V.: A core modeling language for the working molecular biologist (Abstract). In: Priami, C. (ed.) CMSB 2003. LNCS, vol. 2602, pp. 166–166. Springer, Heidelberg (2003)
Curti, M., Degano, P., Baldari, C.T.: Causal π-calculus for biochemical modelling. In: Priami, C. (ed.) CMSB 2003. LNCS, vol. 2602, pp. 21–33. Springer, Heidelberg (2003)
Curti, M., Degano, P., Priami, C., Baldari, C.T.: Modelling biochemical pathways through enhanced π-calculus. Theoretical Computer Science (to appear, 2004)
Degano, P., Priami, C.: Enhanced operational semantics. ACM Computing Surveys 28(2), 352–354 (1996)
Edwards, J.S., Ibarra, R.U., Palsson, B.O.: In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nature Biotechnology 19, 125–130 (2001)
Edwards, J.S., Palsson, B.O.: The Escherichia coli mg1665 in silico metabolic genotype: its definition, characteristics and capabilities. Proceedings of the National Academy of Sciences 97, 5528–5533 (2000)
Fraser, C.M., et al.: The minimal gene complement of mycoplasma genitalium. Science 270(1), 397–403 (1995)
Devlin, T.M., et al.: Textbook of Biochemistry, 5th edn. Wiley and Sons, Inc., Chichester (2002)
Masaru, T., et al.: E–CELL: software environment for whole–cell simulation. Bioinformatics 15, 72–84 (1998)
Fell, D.A.: Understanding the control of metabolism. Portland Press, London, United Kingdom (1997)
Fersht, A.: Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. Freeman, New York (1999)
Hammes, G.G., Shimmel, P.R.: The Enzymes. In: Boyer, P.D. (ed.), vol. 2, Academic Press, New York (1970)
Kitano, H.: Foundations of System Biology. MIT Press, Cambridge (2002)
Koonin, E.V.: How many genes can make a cell: The minimal-gene-set concept. Annuual Review Genomics and Human Genetics 01, 99–116 (2000)
Loew, L.M., Schaff, J.C.: The virtual cell: a software environment for computational cell biology. Trends Biotechnology 19(10), 401–406 (2001)
Milner, R.: Communicating and Mobile Systems: the π-calculus. Cambridge University Press, Cambridge (1999)
Mushegian, A.R., Koonin, E.V.: A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proceedings of National Academy of Science USA 93, 10268–10273 (1996)
Nottegar, C., Priami, C., Degano, P.: Performance evaluation of mobile processes via abstract machines. IEEE Transactions on Software Engineering 27(10), 867–889 (2001)
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 80, 25–31 (2001)
Regev, A., Panina, E.M., Silverman, W., Cardelli, L., Shapiro, E.: Bioambients: An abstraction for biological compartments. Theoretical Computer Science (to appear, 2004)
Regev, A., Shapiro, E.: Cells as computations. Nature 419, 343 (2002)
Regev, A., Silverman, W., Shapiro, E.: Representation and simulation of biochemical processes using the π-calculus process algebra. In: Pacific Symposium of Biocomputing (PSB 2001), pp. 459–470 (2001)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Chiarugi, D., Curti, M., Degano, P., Marangoni, R. (2005). VICE: A VIrtual CEll. In: Danos, V., Schachter, V. (eds) Computational Methods in Systems Biology. CMSB 2004. Lecture Notes in Computer Science(), vol 3082. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-25974-9_16
Download citation
DOI: https://doi.org/10.1007/978-3-540-25974-9_16
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-25375-4
Online ISBN: 978-3-540-25974-9
eBook Packages: Computer ScienceComputer Science (R0)