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13. CMSB 2015: Nantes, France

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Olivier F. Roux, Jérémie Bourdon:
Computational Methods in Systems Biology - 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings. Lecture Notes in Computer Science 9308, Springer 2015, ISBN 978-3-319-23400-7

Invited Talks

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Benoît Barbot, Marta Z. Kwiatkowska, Alexandru Mereacre, Nicola Paoletti:
Estimation and Verification of Hybrid Heart Models for Personalised Medical and Wearable Devices. 3-7
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Gilles Bernot, Jean-Paul Comet, Olivier F. Roux:
A Genetically Modified Hoare Logic that Identifies the Parameters of a Gene Network. 8-12

Regular Papers

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Qinsi Wang, Paolo Zuliani, Soonho Kong, Sicun Gao, Edmund M. Clarke:
SReach: A Probabilistic Bounded Delta-Reachability Analyzer for Stochastic Hybrid Systems. 15-27
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Daniel Trejo-Baños, Andrew J. Millar, Guido Sanguinetti:
Experimental Design for Inference over the A. thaliana Circadian Clock Network. 28-39
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Luca Bortolussi, Dimitrios Milios, Guido Sanguinetti:
Efficient Stochastic Simulation of Systems with Multiple Time Scales via Statistical Abstraction. 40-51
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Carolin Loos, Carsten Marr, Fabian J. Theis, Jan Hasenauer:
Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics. 52-63
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Luca Cardelli, Marta Z. Kwiatkowska, Luca Laurenti:
Stochastic Analysis of Chemical Reaction Networks Using Linear Noise Approximation. 64-76
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Sergiy Bogomolov, Thomas A. Henzinger, Andreas Podelski, Jakob Ruess, Christian Schilling:
Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks. 77-89
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Vivek Nigam, Robin Donaldson, Merrill Knapp, Tim McCarthy, Carolyn L. Talcott:
Inferring Executable Models from Formalized Experimental Evidence. 90-103
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Ovidiu Radulescu, Satya Swarup Samal, Aurélien Naldi, Dima Grigoriev, Andreas Weber:
Symbolic Dynamics of Biochemical Pathways as Finite States Machines. 104-120
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Francy Camacho, Rodrigo Torres, Raúl Ramos-Pollán:
Feature Learning Using Stacked Autoencoders to Predict the Activity of Antimicrobial Peptides. 121-132
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Guillaume Madelaine, Cédric Lhoussaine, Joachim Niehren:
Structural Simplification of Chemical Reaction Networks Preserving Deterministic Semantics. 133-144
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Robert Rozanski, Stefano Bragaglia, Oliver Ray, Ross D. King:
Automating the Development of Metabolic Network Models. 145-156
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Joachim Niehren, Mathias John, Cristian Versari, François Coutte, Philippe Jacques:
Qualitative Reasoning for Reaction Networks with Partial Kinetic Information. 157-169
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Max Ostrowski, Loïc Paulevé, Torsten Schaub, Anne Siegel, Carito Guziolowski:
Boolean Network Identification from Multiplex Time Series Data. 170-181
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Curtis Madsen, Fedor Shmarov, Paolo Zuliani:
BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models. 182-194
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Wassim Abou-Jaoudé, Jérôme Feret, Denis Thieffry:
Derivation of Qualitative Dynamical Models from Biochemical Networks. 195-207
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Pauline Traynard, François Fages, Sylvain Soliman:
Model-Based Investigation of the Effect of the Cell Cycle on the Circadian Clock Through Transcription Inhibition During Mitosis. 208-221
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Chris J. Banks, Daniel D. Seaton, Ian Stark:
Analysis of a Post-translational Oscillator Using Process Algebra and Spatio-Temporal Logic. 222-238
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Alexander Andreychenko, Morgan Magnin, Katsumi Inoue:
Modeling of Resilience Properties in Oscillatory Biological Systems Using Parametric Time Petri Nets. 239-250
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Lubos Brim, Milan Ceska, Martin Demko, Samuel Pastva, David Safránek:
Parameter Synthesis by Parallel Coloured CTL Model Checking. 251-263
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Adam Streck, Kirsten Thobe, Heike Siebert:
Analysing Cell Line Specific EGFR Signalling via Optimized Automata Based Model Checking. 264-276

Short Papers

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Marko Budinich, Jérémie Bourdon, Abdelhalim Larhlimi, Damien Eveillard:
OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques. 279-281
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Etienne Z. Gnimpieba, Mathialakan Thavappiragasam, Abalo Chango, Bill Conn, Carol M. Lushbough:
SBMLDock: Docker Driven Systems Biology Tool Development and Usage. 282-285

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