Computational Methods in Systems Biology : 18th International Conference, CMSB 2020, Konstanz, Germany, September 23-25, 2020, Proceedings.: 18th International Conference, CMSB 2020, Konstanz, Germany, September 23-25, 2020, Proceedings. ([2020])

• Record Type: Book
• Other Names: Abate, Alessandro; Petrov, Tatjana; Wolf, Verena
• 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.
• Publisher Details: Cham, Switzerland : Springer
• Publication Date: 2020
• Extent: 1 online resource
• Subjects: 570.285; Bioinformatics -- Congresses; Electronic books
• Languages: English
• ISBNs: 9783030603274
• Related ISBNs: 303060327X; 3030603261; 9783030603267
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