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Author CMSB (Conference) (18th : 2020 : Online)

Title Computational methods in systems biology : 18th International Conference, CMSB 2020, Konstanz, Germany, September 23-25, 2020, Proceedings / Alessandro Abate, Tatjana Petrov, Verena Wolf (eds.)
Published Cham, Switzerland : Springer, [2020]

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Description 1 online resource
Series Lecture notes in computer science ; 12314
Lecture notes in bioinformatics
LNCS sublibrary, SL 8, Bioinformatics
Lecture notes in computer science ; 12314.
Lecture notes in computer science. Lecture notes in bioinformatics.
LNCS sublibrary. SL 8, Bioinformatics.
Contents Intro -- Preface -- Organization -- Invited Talks -- Context Dependence of Biological Circuits: Predictive Models and Engineering Solutions -- Methods and Tools for the Quantitative Characterization of Engineered Biomolecular Systems -- Employing Immersive Virtual Reality to Reveal Common Geometric Principles of Individual and Collective Decision-Making -- Contents -- Modelling and Analysis -- Rate Equations for Graphs -- 1 Introduction -- 1.1 Two-Legged DNA Walker -- 1.2 Discussion -- 1.3 Relation to the rule-algebraic approach -- 2 Stochastic Graph Rewriting
2.1 The Category of Directed Multigraphs -- 2.2 Graph Rewriting -- 2.3 Composition and Modularity of Derivations -- 2.4 Gluings -- 3 Graph-Based GREs -- 4 Conclusion -- A Pushout and pull-back complements -- B Generalised proofs of lemmas -- B.1 Proof of Lemma 4 (minimal gluings) -- B.2 Proof of Lemma 1 (forward modularity) -- B.3 Proof of Lemma 2 (backward modularity) -- B.4 Proof of Lemma 3 (derivability) -- References -- Stationary Distributions and Metastable Behaviour for Self-regulating Proteins with General Lifetime Distributions -- 1 Introduction -- 2 One-Dimensional Model
3 Multiclass-multistage Model -- 4 Bursting -- 5 Metastable Transitioning -- 6 Discussion -- References -- Accelerating Reactions at the DNA Can Slow Down Transient Gene Expression -- 1 Introduction -- 1.1 Related Works -- 2 Preliminaries -- 3 Moment Calculations -- 3.1 Four-State Chain -- 4 Singular-Perturbation Analysis of the Slow-by-fast Regime -- 4.1 Inner Solution and Matching -- 5 Discussion and Future Work -- References -- Graphical Conditions for Rate Independence in Chemical Reaction Networks -- 1 Introduction -- 2 Preliminaries -- 2.1 Notations -- 2.2 CRN Syntax -- 2.3 CRN Semantics
2.4 Petri Net Structure -- 3 Rate Independence Condition for Persistent Outputs -- 3.1 Sufficient Graphical Condition -- 3.2 Constraint-Based Programming -- 4 Global Rate Independence Condition -- 4.1 Sufficient Graphical Condition -- 4.2 Necessary Condition -- 5 Evaluation on Biomodels -- 5.1 Computation of Rate-Independent Output Species -- 5.2 Test of Global Rate-Independence -- 6 Conclusion -- References -- Interval Constraint Satisfaction and Optimization for Biological Homeostasis and Multistationarity -- 1 Introduction -- 2 Settings and Definitions
3 Interval Methods for Nonlinear Constraint Solving and Optimization -- 3.1 Intervals -- 3.2 Interval Methods for Constraint Solving -- 4 Multistationarity -- 5 IbexHomeo for Finding Homeostatic Species -- 5.1 Interval Branch and Bound Methods for Constrained Global Optimization -- 5.2 A Dedicated Solver for Homeostasis Based on IbexOpt -- 6 Experimental Results -- 7 Discussion and Conclusion -- References -- Growth Dependent Computation of Chokepoints in Metabolic Networks -- 1 Introduction -- 2 Preliminary Concepts and Definitions -- 2.1 Constraint-Based Models -- 2.2 Topological Definitions
Summary 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
Notes International conference proceedings
"The conference was originally planned to be hosted by the University of Konstanz, but due to the COVID-19 pandemic, CMSB 2020 took place fully online."--Preface
2.3 Flux Dependent Definitions
Includes author index
Online resource; title from PDF title page (SpringerLink, viewed December 2, 2020)
Subject Bioinformatics -- Congresses
Bioinformatics
Genre/Form proceedings (reports)
Conference papers and proceedings
Conference papers and proceedings.
Actes de congrès.
Form Electronic book
Author Abate, Alessandro.
Petrov, Tatjana
Wolf, Verena
ISBN 9783030603274
303060327X
Other Titles CMSB 2020