Computational Methods in Systems Biology: 17th International Conference, CMSB 2019, Trieste, Italy, September 18–20, 2019, Proceedings

Front Matter ....Pages i-xi
Front Matter ....Pages 1-1
 Sequential Reprogramming of Boolean Networks Made Practical  (Hugues Mandon, Cui Su, Stefan Haar, Jun Pang, Loïc Paulevé)....Pages 3-19
 Sequential Reprogramming of Biological Network Fate  (Jérémie Pardo, Sergiu Ivanov, Franck Delaplace)....Pages 20-41
 Control Variates for Stochastic Simulation of Chemical Reaction Networks  (Michael Backenköhler, Luca Bortolussi, Verena Wolf)....Pages 42-59
 Effective Computational Methods for Hybrid Stochastic Gene Networks  (Guilherme C. P. Innocentini, Fernando Antoneli, Arran Hodgkinson, Ovidiu Radulescu)....Pages 60-77
 On Chemical Reaction Network Design by a Nested Evolution Algorithm  (Elisabeth Degrand, Mathieu Hemery, François Fages)....Pages 78-95
 Designing Distributed Cell Classifier Circuits Using a Genetic Algorithm  (Melania Nowicka, Heike Siebert)....Pages 96-119
 Extending a Hodgkin-Huxley Model for Larval Drosophila Muscle Excitability via Particle Swarm Fitting  (Paul Piho, Filip Margetiny, Ezio Bartocci, Richard R. Ribchester, Jane Hillston)....Pages 120-139
 Cell Volume Distributions in Exponentially Growing Populations  (Pavol Bokes, Abhyudai Singh)....Pages 140-154
 Transient Memory in Gene Regulation  (Calin Guet, Thomas A. Henzinger, Claudia Igler, Tatjana Petrov, Ali Sezgin)....Pages 155-187
 A Logic-Based Learning Approach to Explore Diabetes Patient Behaviors  (Josephine Lamp, Simone Silvetti, Marc Breton, Laura Nenzi, Lu Feng)....Pages 188-206
 Reachability Design Through Approximate Bayesian Computation  (Mahmoud Bentriou, Paolo Ballarini, Paul-Henry Cournède)....Pages 207-223
 Fast Enumeration of Non-isomorphic Chemical Reaction Networks  (Carlo Spaccasassi, Boyan Yordanov, Andrew Phillips, Neil Dalchau)....Pages 224-247
 A Large-Scale Assessment of Exact Model Reduction in the BioModels Repository  (Isabel Cristina Pérez-Verona, Mirco Tribastone, Andrea Vandin)....Pages 248-265
 Computing Difference Abstractions of Metabolic Networks Under Kinetic Constraints  (Emilie Allart, Joachim Niehren, Cristian Versari)....Pages 266-285
Front Matter ....Pages 287-287
 BRE:IN - A Backend for Reasoning About Interaction Networks with Temporal Logic  (Judah Goldfeder, Hillel Kugler)....Pages 289-295
 The Kappa Simulator Made Interactive  (Pierre Boutillier)....Pages 296-301
 Biochemical Reaction Networks with Fuzzy Kinetic Parameters in Snoopy  (George Assaf, Monika Heiner, Fei Liu)....Pages 302-307
 Compartmental Modeling Software: A Fast, Discrete Stochastic Framework for Biochemical and Epidemiological Simulation  (Christopher W. Lorton, Joshua L. Proctor, Min K. Roh, Philip A. Welkhoff)....Pages 308-314
 Spike – Reproducible Simulation Experiments with Configuration File Branching  (Jacek Chodak, Monika Heiner)....Pages 315-321
 KAMIStudio: An Environment for Biocuration of Cellular Signalling Knowledge  (Russ Harmer, Eugenia Oshurko)....Pages 322-328
 A New Version of DAISY to Test Structural Identifiability of Biological Models  (M. P. Saccomani, G. Bellu, S. Audoly, L. d’Angió)....Pages 329-334
Front Matter ....Pages 335-335
 Semi-quantitative Abstraction and Analysis of Chemical Reaction Networks (Extended Abstract)  (Milan Češka, Jan Křetínský)....Pages 337-341
 Bayesian Parameter Estimation for Stochastic Reaction Networks from Steady-State Observations  (Ankit Gupta, Mustafa Khammash, Guido Sanguinetti)....Pages 342-346
 Wasserstein Distances for Estimating Parameters in Stochastic Reaction Networks  (Kaan Öcal, Ramon Grima, Guido Sanguinetti)....Pages 347-351
 On Inferring Reactions from Data Time Series by a Statistical Learning Greedy Heuristics  (Julien Martinelli, Jeremy Grignard, Sylvain Soliman, François Fages)....Pages 352-355
 Barbaric Robustness Monitoring Revisited for STL* in Parasim  (David Šafránek, Matej Troják, Vojtěch Brůža, Tomáš Vejpustek, Jan Papoušek, Martin Demko et al.)....Pages 356-359
 Symmetry Breaking for GATA-1/PU.1 Model  (Lenka Přibylová, Barbora Losová)....Pages 360-363
 Scalable Control of Asynchronous Boolean Networks  (Cui Su, Soumya Paul, Jun Pang)....Pages 364-367
 Transcriptional Response of SK-N-AS Cells to Methamidophos (Extended Abstract)  (Akos Vertes, Albert-Baskar Arul, Peter Avar, Andrew R. Korte, Lida Parvin, Ziad J. Sahab et al.)....Pages 368-372
 Separators for Polynomial Dynamic Systems with Linear Complexity  (Ines Abdeljaoued-Tej, Alia Benkahla, Ghassen Haddad, Annick Valibouze)....Pages 373-378
 Bounding First Passage Times in Chemical Reaction Networks  (Michael Backenköhler, Luca Bortolussi, Verena Wolf)....Pages 379-382
 Data-Informed Parameter Synthesis for Population Markov Chains  (Matej Hajnal, Morgane Nouvian, Tatjana Petrov, David Šafránek)....Pages 383-386
Back Matter ....Pages 387-388