Description |
1 online resource |
Series |
Lecture notes in computer science ; 12314 |
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Lecture notes in bioinformatics |
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LNCS sublibrary, SL 8, Bioinformatics |
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Lecture notes in computer science ; 12314.
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Lecture notes in computer science. Lecture notes in bioinformatics.
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LNCS sublibrary. SL 8, Bioinformatics.
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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 |
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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 |
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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 |
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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 |
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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 |
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"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 |
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2.3 Flux Dependent Definitions |
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Includes author index |
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Online resource; title from PDF title page (SpringerLink, viewed December 2, 2020) |
Subject |
Bioinformatics -- Congresses
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Bioinformatics
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Genre/Form |
proceedings (reports)
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Conference papers and proceedings
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Conference papers and proceedings.
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Actes de congrès.
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Form |
Electronic book
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Author |
Abate, Alessandro.
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Petrov, Tatjana
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Wolf, Verena
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ISBN |
9783030603274 |
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303060327X |
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