Abate Alessandro, Petrov Tatjana, Wolf Verena (eds.) Computational Methods in Systems Biology: 18th International Conference

Springer, 2020. — xix, 387 p.This book constitutes the refereed proceedings of the 18th International Conference on Computational Methods in Systems Biology, CMSB 2020, held in Konstanz, Germany, in September 2020.
The 17 full papers and 5 tool papers were carefully reviewed and selected from 30 submissions. In addition 3 abstracts of invited talks and 2 tutorials have been included in this volume. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verification, 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; computational approaches for synthetic biology; and case studies in systems and synthetic biology.Rate Equations for Graphs (Vincent Danos, Tobias Heindel, Ricardo Honorato-Zimmer, Sandro Stucki).
Stationary Distributions and Metastable Behaviour for Self-regulating Proteins with General Lifetime Distributions (Candan Çelik, Pavol Bokes, Abhyudai Singh).
Accelerating Reactions at the DNA Can Slow Down Transient Gene Expression (Pavol Bokes, Julia Klein, Tatjana Petrov).
Graphical Conditions for Rate Independence in Chemical Reaction Networks (Élisabeth Degrand, François Fages, Sylvain Soliman).
Interval Constraint Satisfaction and Optimization for Biological Homeostasis and Multistationarity (Aurélien Desoeuvres, Gilles Trombettoni, Ovidiu Radulescu).
Growth Dependent Computation of Chokepoints in Metabolic Networks (Alexandru Oarga, Bridget Bannerman, Jorge Júlvez).
On the Complexity of Quadratization for Polynomial Differential Equations (Mathieu Hemery, François Fages, Sylvain Soliman).
Comparing Probabilistic and Logic Programming Approaches to Predict the Effects of Enzymes in a Neurodegenerative Disease Model (Sophie Le Bars, Jérémie Bourdon, Carito Guziolowski).
Control Strategy Identification via Trap Spaces in Boolean Networks (Laura Cifuentes Fontanals, Elisa Tonello, Heike Siebert)...Pages 159-175
Qualitative Analysis of Mammalian Circadian Oscillations: Cycle Dynamics and Robustness (Ousmane Diop, Madalena Chaves, Laurent Tournier).
Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision (Stéphanie Chevalier, Vincent Noël, Laurence Calzone, Andrei Zinovyev, Loïc Paulevé).
Classifier Construction in Boolean Networks Using Algebraic Methods (Robert Schwieger, Matías R. Bender, Heike Siebert, Christian Haase).
Sequential Temporary and Permanent Control of Boolean Networks (Cui Su, Jun Pang).
ABC(SMC)\(^2\): Simultaneous Inference and Model Checking of Chemical Reaction Networks (Gareth W. Molyneux, Alessandro Abate).
Parallel Parameter Synthesis for Multi-affine Hybrid Systems from Hybrid CTL Specifications (Eva àmijáková, Samuel Pastva, David àafránek, Luboš Brim).
Core Models of Receptor Reactions to Evaluate Basic Pathway Designs Enabling Heterogeneous Commitments to Apoptosis (Marielle Péré, Madalena Chaves, Jérémie Roux)...Pages 298-320
Drawing the Line: Basin Boundaries in Safe Petri Nets (Stefan Haar, Loïc Paulevé, Stefan Schwoon)
ModRev - Model Revision Tool for Boolean Logical Models of Biological Regulatory Networks (Filipe Gouveia, Inês Lynce, Pedro T. Monteiro)...Pages 339-348
fnyzer: A Python Package for the Analysis of Flexible Nets (Jorge Júlvez, Stephen G. Oliver).
eBCSgen: A Software Tool for Biochemical Space Language (Matej Troják, David àafránek, Lukrécia Mertová, Luboš Brim).
What is a Cell Cycle Checkpoint? The TotemBioNet Answer (Déborah Boyenval, Gilles Bernot, Hélène Collavizza, Jean-Paul Comet).
Kaemika App: Integrating Protocols and Chemical Simulation (Luca Cardelli).