Full Description
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.
* The conference was held virtually due to the COVID-19 pandemic.
Contents
Modelling and Analysis.- Rate Equations For Graphs.- Stationary Distributions and Metastable Behaviour for Self-Regulating Proteins with General Lifetime Distributions.- Accelerating Reactions at the DNA Can Slow Down Transient Gene Expression.- Graphical Conditions for Rate Independence in Chemical Reaction Networks.- Interval Constraint Satisfaction and Optimization for Biological Homeostasis and Multistationarity.- Growth Dependent Computation of Chokepoints in Metabolic Networks.- On the Complexity of Quadratization for Polynomial Differential Equations.- Comparing Probabilistic and Logic Programming Approaches to Predict the Effects of Enzymes in a Neurogenerative Disease Model.- Boolean Networks.- Control Strategy Identification via Trap Spaces in Boolean Networks.- Qualitative Analysis of Mammalian Circadian Oscillations: Cycle Dynamics and Robustness.- Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision.- Classifier Construction in Boolean Networks Using Algebraic Methods.- Sequential Temporary and Permanent Control of Boolean Networks.- Inference and Identification.- ABC(SMC)^2: Simultaneous Inference and Model Checking of Chemical Reaction Networks.- Parameter Synthesis for Hybrid Systems from Hybrid CTL Specifications.- Core Models of Receptor Reactions Evaluate Basic Pathway Designs Enabling Heterogeneous Commitments to Apoptosis.- Drawing the Line: Basin Boundaries in Safe Petri Nets.- Tools.- ModRev - Model Revision Tool for Boolean Logical Models of Biological Regulatory Networks.- fnyzer: a Python Package for the Analysis of Flexible Nets.- eBCSgen: A Software Tool for Biochemical Space Language.- What is a Cell Cycle Checkpoint ? The TotemBioNet Answer.- Kaemika App, Integrating Protocols and Chemical Simulation.- Tutorials.- Tutorial: The CoLoMoTo Interactive Notebook, Accessible and Reproducible Computational Analyses for Qualitative Biological Networks.- Integrating Experimental Pharmacology and Systems Biology for GPCR Drug Discovery.
