Get Computational Methods in Systems Biology: International PDF

By Marino Miculan, Giorgio Bacci (auth.), Corrado Priami (eds.)

ISBN-10: 3540461663

ISBN-13: 9783540461661

This e-book constitutes the refereed complaints of the overseas convention on Computational equipment in structures Biology, CMSB 2006, held in Trento, Italy, in October 2006.The 22 revised complete papers awarded including 2 invited talks have been conscientiously reviewed and chosen from sixty eight submissions. The papers current quite a few suggestions from desktop technological know-how, reminiscent of language layout, concurrency idea, software program engineering, and formal tools, for biologists, physicists, and mathematicians drawn to the systems-level figuring out of mobile methods

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Extra resources for Computational Methods in Systems Biology: International Conference, CMSB 2006, Trento, Italy, October 18-19, 2006. Proceedings

Example text

P ) = nl(P ) Definition 15. σ) 28 N. t. →) of a process in normal form is finite. This fact will be used to show that the quasi-orders on processes and on systems are wqo. Definition 16. Let P be a system in normal form. t. → is defined as follows: nf Deriv(P ) = {P | P →∗ P }. The following lemma provides an upper bound to the nesting level of the derivatives of a system P : Lemma 3. Let P be a systems in normal form and let P ∈ nf Deriv(P ). Then nl(P ) ≤ nl(P ) + ndpino(P ). We introduce a quasi-order τ if proc on processes in normal form such that σ proc – for each occurrence of a replicated guarded process at top-level in σ there is a corresponding occurrence of the same process at top-level in τ ; – for each occurrence of a guarded process at top-level in σ there is either a corresponding occurrence of the same process or an occurrence of the replicated version of the process at top-level in τ .

E. we do not require any other module to synchronise on these commands. The guards of these commands incorporate dependencies on the current state both of FRS2 itself and of other compounds. More precisely, FGFR must be bound to FRS2 and certain receptors of FGFR must have already been phosphorylated. g. the release of Src (the commands labelled src rel ) and the binding and release of Sos (the commands labelled sos bind frs and sos rel frs). Note the corresponding commands in modules SRC (Figure 5) and SOS (Figure 6).

Hence, exploiting the results in section 3, we obtain decidability of termination. We note that each system (resp. (σ Q ) (resp. σ). (σ Q ) of a system R is simpler than R. More precisely, the maximum nesting level of membranes in Q is strictly smaller than the maximum nesting level of membranes in R. As already observed in [6], the reactions in MBD preserve the nesting level of membranes. The only operation that can increase the nesting level of membranes is pino. However, we note that the number of pino operations nested one inside the other in the processes of a system is bounded.

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Computational Methods in Systems Biology: International Conference, CMSB 2006, Trento, Italy, October 18-19, 2006. Proceedings by Marino Miculan, Giorgio Bacci (auth.), Corrado Priami (eds.)


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