Abstract
The aim of this work is twofold. First, we propose an high level textual modelling language, which is meant to be biologically intuitive and hence easily usable by life scientists in modelling intra-cellular systems. Secondly, we provide an automatic translation of the proposed language into Beta-binders, a bio-inspired process calculus, which allows life scientists to formally analyse and simulate their models. We use the Gp130 signalling pathway as a case study.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Milner, R.: Communication and Concurrency. Prentice-Hall, Englewood Cliffs (1989)
Priami, C., Regev, A., Silverman, W., Shapiro, E.: Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 80(1), 25–31 (2001)
Phillips, A., Cardelli, L.: A Correct Abstract Machine for the Stochastic Pi-calculus. In: BioConcur 2004, Workshop on Concurrent Models in Molecular Biology (2004)
Priami, C., Quaglia, P.: Operational patterns in Beta-binders. Transactions on Computational Systems Biology 1, 50–65 (2005)
Calder, M., Gilmore, S., Hillston, J.: Modelling the Influence of RKIP on the ERK Signalling Pathway Using the Stochastic Process Algebra PEPA. T. Comp. Sys. Biology 7, 1–23 (2006)
Kwiatkowska, M., Norman, G., Parker, D., Tymchyshyn, O., Heath, J., Gaffney, E.: Simulation and verification for computational modelling of signalling pathways. In: Proc. Winter Simulation Conference, Omnipress, pp. 1666–1675 (2006)
Kholodenko, B.: Cell signalling dynamics in time and space. Nature Reviews Molecular Cell Biology 7(3), 165–176 (2006)
Kohn, K.: Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems. Molecular Biology of the Cell 10, 2703–2734 (1999)
Kitano, H.: A graphical notation for biochemical networks. Biosilico 1(5), 169–176 (2003)
Romanel, A., Dematté, L., Priami, C.: The Beta Workbench. Technical Report TR-03-2007. Technical report, The Microsoft Research - University of Trento Centre for Computational and Systems Biology (2007)
Hucka, M., Finney, A., Sauro, H., Bolouri, H., Doyle, J., Kitano, H.: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524–531 (2003)
Underhill-Day, N., Heath, J.: Oncostatin M (OSM) Cytostasis of Breast Tumor Cells: Characterization of an OSM Receptor β-Specific Kernel. Cancer Research 66(22), 10891–10901 (2006)
Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P.: Molecular biology of the cell. Garland Science (2002)
Cardelli, L.: On Process Rate Semantics (2007), available at http://lucacardelli.name/Papers/On%20Process%20Rate%20Semantics.pdf
Ciocchetta, F., Priami, C.: Beta-binders with Biological Transactions. Technical Report TR-10-2006. Technical report, The Microsoft Research - University of Trento Centre for Computational and Systems Biology (2006)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Guerriero, M.L., Heath, J.K., Priami, C. (2007). An Automated Translation from a Narrative Language for Biological Modelling into Process Algebra. In: Calder, M., Gilmore, S. (eds) Computational Methods in Systems Biology. CMSB 2007. Lecture Notes in Computer Science(), vol 4695. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-75140-3_10
Download citation
DOI: https://doi.org/10.1007/978-3-540-75140-3_10
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-75139-7
Online ISBN: 978-3-540-75140-3
eBook Packages: Computer ScienceComputer Science (R0)