Download PDF by Pedro Mendes, Joseph O. Dada, Kieran Smallbone: Computational Methods in Systems Biology: 12th International

By Pedro Mendes, Joseph O. Dada, Kieran Smallbone

ISBN-10: 3319129813

ISBN-13: 9783319129815

ISBN-10: 3319129821

ISBN-13: 9783319129822

This booklet constitutes the lawsuits of the twelfth overseas convention on Computational equipment in platforms Biology, CMSB 2014, held in Manchester, united kingdom, in November 2014.
The sixteen typical papers offered including 6 poster papers have been conscientiously reviewed and chosen from 31 standard and 18 poster submissions. The papers are geared up in topical sections on formalisms for modeling organic strategies, version inference from experimental info, frameworks for version verification, validation, and research of organic platforms, types and their organic functions, computational techniques for man made biology, and flash posters.

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Extra resources for Computational Methods in Systems Biology: 12th International Conference, CMSB 2014, Manchester, UK, November 17-19, 2014, Proceedings

Example text

Therefore, t does not satisfy IZP and one returns false. Otherwise, there exists a j ∈ U such that Kj = 0 thanks to Theorem 4, so there exists a column w of K such that wj = 0. It may happen that wj is not solution of (S). In that case, consider a nonzero solution u of (S) with at least two nonzero coefficients. By a topology argument, the vector u ¯ = u + ε1 w is also solution of (S) for any rational ε1 satisfying |ε1 | < ε (where ε is a small rational). Finally, one can choose a suitable ε1 to obtain the condition u¯j = 0, and (S) satisfies IZP.

4 Validating the Pathway with the Stoichiometry Using SMT To check if the pathway obtained with SAT is consistent with the stoichiometry of the network, we examine if it is contained in the kernel of the stoichiometric matrix. At this step, the pathway is represented by a set of reactions. If this pathway is consistent with the stoichiometry of the network, there exists a vector with non-null coefficients belonging to the kernel of the sub-matrix of the set of reactions of the pathway. If the solution vector (which represents the pathway) has only strictly positive values or only strictly negative value, it is selected to be a potential solution of the network.

Applications of network-based pathway analyses have been presented for predicting functional properties of metabolic networks, measuring different aspects of robustness and flexibility, and even assessing gene regulatory features [35,14]. Actually, EFMs can only be enumerated in small to medium-scale metabolic networks because the number of EFMs increase exponentially P. Mendes et al. ): CMSB 2014, LNBI 8859, pp. 20–31, 2014. c Springer International Publishing Switzerland 2014 SAT-Based Metabolics Pathways Analysis without Compilation 21 with the network size [21].

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Computational Methods in Systems Biology: 12th International Conference, CMSB 2014, Manchester, UK, November 17-19, 2014, Proceedings by Pedro Mendes, Joseph O. Dada, Kieran Smallbone


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