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This book constitutes the refereed proceedings of the 19th International Conference on Computational Methods in Systems Biology, CMSB 2021, held in Bordeaux, France, September 22-24, 2021.*The 13 full papers and 5 tool papers were carefully reviewed and selected from 32 submissions. The topics of interest include biological process modelling; biological system model verification, validation, analysis, and simulation; high-performance computational systems biology; model inference from experimental data; multi-scale modeling and analysis methods; computational approaches for synthetic biology; machine learning and data-driven approaches; microbial ecology modelling and analysis; methods and protocols for populations and their variability; models, applications, and case studies in systems and synthetic biology. The chapters "Microbial Community Decision Making Models in Batch", "Population design for synthetic gene circuits", "BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems" are published open access under a CC BY license (Creative Commons Attribution 4.0 International License).
* The conference was held in a hybrid mode due to the COVID-19 pandemic.
List of contents
Reducing Boolean Networks with Backward Boolean Equivalence.- Abstraction of Markov Population Dynamics via Generative Adversarial Nets.- Greening R. Thomas' Framework with Environment Variables: a Divide and Conquer Approach.- Automated inference of production rules for glycans.- Compiling Elementary Mathematical Functions into Finite Chemical Reaction Networks via a Polynomialization Algorithm for ODEs.- Interpretable exact linear reductions via positivity.- Explainable artificial neural network for recurrent venous thromboembolism based on plasma proteomics.- Neural networks to predict survival from RNA-seq data in oncology.- Microbial Community Decision Making Models in Batchand Chemostat Cultures.-Learning Boolean controls in regulated metabolic networks: a case-study.- Population design for synthetic gene circuits.- Nonlinear pattern matching in rule-based modeling languages.- Protein noise and distribution in a two-stage gene-expression model extended by an mRNA inactivation loop.- Aeon 2021: Bifurcation Decision Trees in Boolean Networks.- LNetReduce: tool for reducing linear dynamic networks with separated time scales.- ppsim: A software package for efficiently simulating and visualizing population protocols.- Web-based Structural Identifiability Analyzer BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems.
