Abstract
The complexity of biological systems is at times made worse by the diversity of ways in which they are described: the organic evolution of the science over many years has led to a myriad of conventions. This confusion is reflected by the in-silico representation of biological models, where many different computational paradigms and formalisms are used in a variety of software tools.
The Systems Biology Markup Language (SBML) is an attempt to overcome this issue and aims to simplify the exchange of information by imposing a standardized way of representing models. The success of the idea is attested to by the fact that more than 110 software tools currently support SBML in one form or another.
This work focuses on the translation of the Cyto-Sim simulation language (based on a discrete stochastic implementation of P systems) to SBML. We consider the issues both from the point of view of the employed software architecture and from that of the mapping between the features of the Cyto-Sim language and those of SBML.
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References
Altman, R.B., et al.: Ribonucleic acid markup language (2002), http://www.smi.stanford.edu/projects/helix/riboml/
Bergmann, F.T., Sauro, H.M.: Sbw - a modular framework for systems biology. In: Proceedings of the 37th conference on Winter simulation. Winter Simulation Conference, pp. 1637–1645 (2006)
Cavaliere, M., Sedwards, S.: Modelling cellular processes using membrane systems with peripheral and integral proteins. In: Priami, C. (ed.) CMSB 2006. LNCS (LNBI), vol. 4210, pp. 108–126. Springer, Heidelberg (2006)
Cuellar, A.A., Lloyd, C.M., Nielsen, P.F., Bullivant, D.P., Nickerson, D.P., Hunter, P.J.: An overview of cellml 1.1, a biological model description language. Simulation 79(12), 740–747 (2003)
Deckard, A., Bergmann, F.T., Sauro, H.M.: Supporting the sbml layout extension. Bioinformatics 22(23), 2966–2967 (2006)
Eccher, C., Priami, C.: Design and implementation of a tool for translating sbml into the biochemical stochastic pi-calculus. Bioinformatics 22(24), 3075–3308 (2006)
Fenyo, D.: The biopolymer markup language. Bioinformatics 15(4), 339–340 (1999)
Finney, A.M., Hucka, M.: Systems biology markup language: Level 2 and beyond. Biochem. Soc. Trans. 31, 1472–1473 (2003)
Project GlassFish: The jaxb project. https://jaxb.dev.java.net/
Hanisch, D., Zimmer, R., Lengauer, T.: Proml - the protein markup language for specification of protein sequences, structures and families. In Silico Biology 2(3), 313–324 (2002)
Hedley, W.J., Nelson, M.R., Bullivant, D.P., Nielson, P.F.: A short introduction to cellml. Philos. Trans. R. Soc. Lond. A 359, 1073–1089 (2001)
Hermjakob, H., et al.: The hupopsiŠs molecular interaction format - a community standard for the representation of protein interaction data. Nature Biotechnol. 22(2), 177–183 (2004)
Hucka, M., et al.: The systems biology markup language (sbml): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4), 524–531 (2003)
Doubletwist Inc.: Agave: architecture for genomic annotation, visualization and exchange (2001), http://www.agavexml.org
LabBook Inc.: Bsml (bioinformatics sequence markup language) 2.2 (2002), http://www.labbook.com/products/xmlbsml.asp
Joshi-Tope, G., Gillespie, M., Vastrik, I., D’Eustachio, P., Schmidt, E., de Bono, B., Jassal, B., Gopinath, G.R., Wu, G.R., Matthews, L., Lewis, S., Birney, E., Stein, L.: Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 33, D428–D432 (2005)
Kanehisa, M., Goto, S.: Kegg: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28(1), 27–30 (2000)
Keating, S.M., Bornstein, B.J., Finney, A., Hucka, M.: Sbmltoolbox: an sbml toolbox for matlab users. Bioinformatics 22(10), 1275–1277 (2006)
Kholodenko, B.N.: Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur. J. Biochem 267, 1583–1588 (2000)
Kleingeld, P., Brown, E.: Cosmopolitanism. In: The Stanford Encyclopedia of Philosophy, Edward N. Zalta (winter 2006)
Le Novère, N., Bornstein, B., Broicher, A., Courtot, M., Donizelli, M., Dharuri, H., Li, L., Sauro, H., Schilstra, M., Shapiro, B., Snoep, J.L., Hucka M.: Biomodels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research 34, D689–D691 (2006)
Liao, Y.M., Ghanadan, H.: The chemical markup language. Anal. Chem. 74(13), 389A-390A (2002)
Machné, R., Finney, A., Müller, S., Lu, J., Widder, S., Flamm, C.: The sbml ode solver library: a native api for symbolic and fast numerical analysis of reaction networks. Bioinformatics 22(11), 1406–1407 (2006)
McArthur, D.C.: An extensible xml schema definition for automated exchange of protein data: Proximl (protein extensible markup language) (2001), http://www.cse.ucsc.edu/douglas/proximl/
Mendes, P.: Gepasi: a software package for modeling the dynamics, steady states, and control of biochemical and other systems. Comput. Applic. Biosci. 9, 563–571 (1993)
Mi, H., Lazareva-Ulitsky, B., Loo, A., Kejariwal, R., Vandergriff, J., Rabkin, S., Guo, N., Muruganujan, A., Doremieux, O., Campbell, M.J.: The panther database of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 33, D284–D288 (2005)
The Microsoft Research University of Trento. Centre for Computational and Systems Biology. Web page of Cyto-Sim (2006), http://www.cosbi.eu/Rpty_Soft_CytoSim.php
Olivier, B.G., Snoep, J.L.: Web-based modelling using jws online. Bioinformatics 20, 2143–2144 (2004)
Apache XML project: Xerces2 java parser 2.9.0 (2004), http://xml.apache.org/xerces2-j/
Rodriguez, N., Donizelli, M., Le Novère, N.: Sbmleditor: effective creation of models in the systems biology markup language (sbml). Bioinformatics 8(79) (published online March 2007)
Rohwer, J.M., Meadowi, N.D., Rosemani, S., Westerhoff, H.V., Postma, P.W.: Understanding glucose transport by the bacterial phosphoenolpyruvate: glycose phosphotransferase system on the basis of kinetic measurements in vitro. The Journal of Biological Chemistry 275(45), 34909–34921 (2000)
Schilstra, M.J., Li, L., Matthews, J., Finney, A., Hucka, M., Le Novère, N.: Cellml2sbml: conversion of cellml into sbml. Bioinformatics 22(8), 1018–1020 (2006)
Shapiro, B.E., Hucka, M., Finney, A., Doyle, J.: Mathsbml: a package for manipulating sbml-based biological models. Bioinformatics 20(16), 2829–2831 (2004)
Spellman, P.T., Miller, M.: Design and implementation of microarray gene expression markup language (mage-ml). Genome Biol. 3(9), 0046.0041–0046.0049 (2002)
Taylor, C.F., Paton, N.W.: A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nature Biotechnol. 21, 247–254 (2003)
Zhike, Z., Klipp, E.: Sbml-pet: a systems biology markup language-based parameter estimation tool. Bioinformatics 22(21), 2704–2705 (2006)
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Mazza, T. (2007). Towards a Complete Covering of SBML Functionalities. In: Eleftherakis, G., Kefalas, P., Păun, G., Rozenberg, G., Salomaa, A. (eds) Membrane Computing. WMC 2007. Lecture Notes in Computer Science, vol 4860. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77312-2_22
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DOI: https://doi.org/10.1007/978-3-540-77312-2_22
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