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By Sergio Pozzi, Gianluca Della Vedova, Giancarlo Mauri (auth.), Vincent Danos, Vincent Schachter (eds.)

The Computational equipment in platforms Biology (CMSB) workshop sequence used to be proven in 2003 through Corrado Priami. the aim of the workshop sequence is to assist catalyze the convergence among machine scientists drawn to language layout, concurrency thought, software program engineering or application verification, and physicists, mathematicians and biologists drawn to the systems-level realizing of mobile methods. platforms biology was once perceived as being more and more looking for subtle modeling frameworks even if for representing and processing syst- point dynamics or for version research, comparability and refinement. One has the following a uncomplicated case of a must-explore box of software for the formal tools built in computing device technology within the final decade. This complaints includes papers from the CMSB 2003 workshop. a very good 3rd of the 24 papers released right here have a special formal equipment beginning; we take this as a affirmation synergy is construction that might support solidify CMSB as a discussion board for cross-community alternate, thereby beginning new theoretical avenues and making the sphere much less of a possible software and extra of a true one. ebook in Springer's new Lecture Notes in Bioinformatics (LNBI) bargains specific visibility and influence, which we gratefully recognize. Our keynote audio system, Alfonso Valencia and Trey Ideker, gave hard and a little bit humbling lectures: they made it transparent that robust purposes to platforms biology are nonetheless a way forward. We thank all of them the extra for accepting the invitation to talk and for the readability and pleasure they dropped at the conference.

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Additional resources for Computational Methods in Systems Biology: International Conference CMSB 2004, Paris, France, May 26-28, 2004, Revised Selected Papers

Sample text

We neglect the regulation at the donor sites because these seem to be less regulated than the acceptor sites [7, 5]. The four acceptor sites are in competition for the regulatory protein allocation. We consider this regulation level only on a single-site scale. Thus we assume the local behaviour as a continuous competition between four acceptor sites. The 46 A. Bockmayr et al. choice of one of them depends on the score of the splice efficiency defined as the ratio of the mature RNA and pre-mRNA at each splicing site [8].

Here, eff 3 (hnRNPA1 ) (resp. eff 7 (hnRNPA1 , rev)) are abbreviated by eff 3 (resp. eff 7 ). The vector u = (env, tat1, rev, nef , tat2)T ∈ IR5≥0 evolves in state i according to the system of differential equations dui /dt = ri · rna, duj /dt = 0, for j = i (Si ) with rate constants r1 , . . , r5 > 0. e. drnatot /dt = 0 (3) Using default reasoning, the continuous dynamics in state i is given by the system of differential equations Si , together with the equations (1) and (2) from Sect. 3, and (3). Table 1.

Following [10], we describe A5 as a preferential activated site in the presence of regulatory proteins, and A4 as the default splicing site. 4 Integrative Model To model the global alternative splicing regulation according to the hypotheses introduced in Sect. 3, we use an hybrid automaton with default reasoning, called A, which is given in Fig. 2. There are five states corresponding to the production (after splicing) of the mRNAs rev, env, nef, tat1, tat2 for the proteins Rev, Env, Nef, Tat with 1 exon, and Tat with 2 exons, respectively.

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