Computational Methods in Systems Biology: International by Marino Miculan, Giorgio Bacci (auth.), Corrado Priami (eds.)

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

This ebook constitutes the refereed court cases of the foreign convention on Computational equipment in platforms Biology, CMSB 2006, held in Trento, Italy, in October 2006.The 22 revised complete papers provided including 2 invited talks have been rigorously reviewed and chosen from sixty eight submissions. The papers current various thoughts from machine technological know-how, akin to language layout, concurrency thought, software program engineering, and formal tools, for biologists, physicists, and mathematicians drawn to the systems-level figuring out of mobile procedures

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6 Property Specification Our primary goal in this case study is to analyse the various mechanisms previously reported to negatively regulate signalling. Since the binding of Grb2 to FRS2 serves as the primary link between FGFR activation and ERK signalling, we examine the amount of Grb2 bound to FRS2 as the system evolves. In addition, we investigate the different causes of degradation which, based on the system description, can be caused by one of the following reactions occurring: – when Src:FRS2 is present, FRS2 is relocated (reaction 8); – when Plc:FGFR is present, it degrades FGFR (reaction 9); – when phosphoSpry binds to Cbl, it degrades FRS2 (reaction 12).

The dual Y653/654 form of the receptor leads to phosphorylation of other FGFR receptor residues: Y663, Y583, Y585, Y766 (in this model we only consider Y766 further). 4. and 5. The dual Y653/654 form of the receptor also leads to phosphorylation of the FGFR substrate FRS2, which binds to both the phosphorylated and dephosphorylated forms of the FGFR. 6. FRS2 can also be dephosphorylated by a phosphotase, denoted Shp2. 7. A number of effector proteins interact with the phosphorylated form of FRS2.

For further details, see [14]. 3 Modelling a Simple Biological System in PRISM We now illustrate PRISM’s modelling and specification languages through an example: the simple set of biological reactions given in Figure 1(a). We consider two Probabilistic Model Checking of Complex Biological Pathways 35 proteins A and B which can undergo complexation with rate r1 and decomplexation with rate r2 . In addition, A can degrade with rate r3 . We give two alternative approaches for modelling these reactions in PRISM, shown in Figures 1(b) and 1(c), respectively.

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