Computational Methods in Systems Biology: 15th International Conference, CMSB 2017, Darmstadt, Germany, September 2729, 2017, Proceedings (Lecture Notes in Computer Science Book 10545)

This book constitutes the refereed proceedings of the 15th International Conference on Computational Methods in Systems Biology, CMSB 2017, held in Darmstadt, Germany, in September 2017. The 15 full papers, 4 tool papers and 4 posters presented together with 1 invited talk were carefully reviewed and selected from 41 regular paper submissions. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verication, validation, analysis, and simulation of biological systems; high-performance computational systems biology and parallel implementations; model inference from experimental data; model integration from biological databases; multi-scale modeling and analysis methods; and computational approaches for synthetic biology. Read more... Abstract: This book constitutes the refereed proceedings of the 15th International Conference on Computational Methods in Systems Biology, CMSB 2017, held in Darmstadt, Germany, in September 2017. The 15 full papers, 4 tool papers and 4 posters presented together with 1 invited talk were carefully reviewed and selected from 41 regular paper submissions. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verication, validation, analysis, and simulation of biological systems; high-performance computational systems biology and parallel implementations; model inference from experimental data; model integration from biological databases; multi-scale modeling and analysis methods; and computational approaches for synthetic biology Front Matter ....Pages I-XIII Front Matter ....Pages 1-1 Bio-Curation for Cellular Signalling: The KAMI Project (Russ Harmer, Yves-Stan Le Cornec, Sébastien Légaré, Ievgeniia Oshurko)....Pages 3-19 Front Matter ....Pages 21-21 Quantitative Regular Expressions for Arrhythmia Detection Algorithms (Houssam Abbas, Alena Rodionova, Ezio Bartocci, Scott A. Smolka, Radu Grosu)....Pages 23-39 Detecting Attractors in Biological Models with Uncertain Parameters (Jiří Barnat, Nikola Beneš, Luboš Brim, Martin Demko, Matej Hajnal, Samuel Pastva et al.)....Pages 40-56 Abduction Based Drug Target Discovery Using Boolean Control Network (Célia Biane, Franck Delaplace)....Pages 57-73 Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data (Arthur Carcano, François Fages, Sylvain Soliman)....Pages 74-90 Identifying Functional Families of Trajectories in Biological Pathways by Soft Clustering: Application to TGF-\(\beta \) Signaling (Jean Coquet, Nathalie Theret, Vincent Legagneux, Olivier Dameron)....Pages 91-107 Strong Turing Completeness of Continuous Chemical Reaction Networks and Compilation of Mixed Analog-Digital Programs (François Fages, Guillaume Le Guludec, Olivier Bournez, Amaury Pouly)....Pages 108-127 A Scheme for Adaptive Selection of Population Sizes in Approximate Bayesian Computation - Sequential Monte Carlo (Emmanuel Klinger, Jan Hasenauer)....Pages 128-144 Methods to Expand Cell Signaling Models Using Automated Reading and Model Checking (Kai-Wen Liang, Qinsi Wang, Cheryl Telmer, Divyaa Ravichandran, Peter Spirtes, Natasa Miskov-Zivanov)....Pages 145-159 A Stochastic Model for the Formation of Spatial Methylation Patterns (Alexander Lück, Pascal Giehr, Jörn Walter, Verena Wolf)....Pages 160-178 Temporal Reprogramming of Boolean Networks (Hugues Mandon, Stefan Haar, Loïc Paulevé)....Pages 179-195 Detecting Toxicity Pathways with a Formal Framework Based on Equilibrium Changes (Benjamin Miraglio, Gilles Bernot, Jean-Paul Comet, Christine Risso-de Faverney)....Pages 196-213 Data-Driven Robust Control for Type 1 Diabetes Under Meal and Exercise Uncertainties (Nicola Paoletti, Kin Sum Liu, Scott A. Smolka, Shan Lin)....Pages 214-232 Graph Representations of Monotonic Boolean Model Pools (Robert Schwieger, Heike Siebert)....Pages 233-248 Explaining Response to Drugs Using Pathway Logic (Carolyn Talcott, Merrill Knapp)....Pages 249-264 Automated Property Synthesis of ODEs Based Bio-pathways Models (Jun Zhou, R. Ramanathan, Weng-Fai Wong, P. S. Thiagarajan)....Pages 265-282 Front Matter ....Pages 283-283 TransferEntropyPT: An R Package to Assess Transfer Entropies via Permutation Tests (Patrick Boba, Kay Hamacher)....Pages 285-290 KaDE: A Tool to Compile Kappa Rules into (Reduced) ODE Models (Ferdinanda Camporesi, Jérôme Feret, Kim Quyên Lý)....Pages 291-299 Database of Dynamic Signatures Generated by Regulatory Networks (DSGRN) (Bree Cummins, Tomas Gedeon, Shaun Harker, Konstantin Mischaikow)....Pages 300-308 Pint: A Static Analyzer for Transient Dynamics of Qualitative Networks with IPython Interface (Loïc Paulevé)....Pages 309-316 Back Matter ....Pages 317-332