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Computational Methods in Systems Biology [[electronic resource] ] : 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings / / edited by Olivier Roux, Jérémie Bourdon
| Computational Methods in Systems Biology [[electronic resource] ] : 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings / / edited by Olivier Roux, Jérémie Bourdon |
| Edizione | [1st ed. 2015.] |
| Pubbl/distr/stampa | Cham : , : Springer International Publishing : , : Imprint : Springer, , 2015 |
| Descrizione fisica | 1 online resource (XIX, 288 p. 81 illus.) |
| Disciplina | 570.285 |
| Collana | Lecture Notes in Bioinformatics |
| Soggetto topico |
Bioinformatics
Computers Computer simulation Bioinformatics Computational biology Software engineering Computer science—Mathematics Computational Biology/Bioinformatics Computation by Abstract Devices Simulation and Modeling Computer Appl. in Life Sciences Software Engineering Symbolic and Algebraic Manipulation |
| ISBN | 3-319-23401-3 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Intro -- Preface -- Organization -- Invited Talks -- Estimation and Verification of Hybrid Heart Models for Personalised Medical and Wearable Devices -- More Thoughts on the Whole Organism Challenge -- A Genetically Modified Hoare Logic that Identifies the Parameters of a Gene Network -- Perspectives on Genome Scale Modelling of Metabolism -- Contents -- Invited Talks -- Estimation and Verification of Hybrid Heart Models for Personalised Medical and Wearable Devices -- 1 Heart Model and Personalisation -- 2 Applications and Discussion -- References -- A Genetically Modified Hoare Logic that Identifies the Parameters of a Gene Network -- 1 Thomas' Gene Regulatory Networks with Multiplexes -- 2 Hoare Triples for Gene Networks -- 3 A Hoare Logic for Gene Networks -- 4 Example -- References -- Regular Papers -- SReach: A Probabilistic Bounded Delta-Reachability Analyzer for Stochastic Hybrid Systems -- 1 Introduction -- 2 Stochastic Hybrid Models -- 3 SReach Algorithm -- 4 Experiments -- 5 Conclusions and Future Work -- References -- Experimental Design for Inference over the A. thaliana Circadian Clock Network -- 1 Introduction -- 2 Methods -- 2.1 Bayesian Experimental Design -- 2.2 Frequency-Domain Model of Gene Expression Levels -- 2.3 Experimental Design for Estimating Parameters of a DSS Model -- 2.4 A. thaliana Circadian Clock Model -- 3 Results -- 4 Conclusions -- References -- Efficient Stochastic Simulation of Systems with Multiple Time Scales via Statistical Abstraction -- 1 Introduction -- 2 Background and Related Work -- 3 Quasi-Equilibrium Reduction -- 4 Approximation of Rate Expectations -- 4.1 Continuity of Rates of the Slow System -- 4.2 Exploring Rate Expectation via Pre-simulation Runs -- 4.3 Stochastic Simulation via Statistical Abstraction -- 5 Experimental Evaluation -- 5.1 Stiff Enzyme-Substrate Reaction.
5.2 Viral Infection Model -- 6 Conclusions -- References -- Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics -- 1 Introduction -- 2 Introduction to Approximate Bayesian Computation -- 3 ABC with Multivariate Test Statistics -- 3.1 Multivariate Test Statistics -- 3.2 Comparison of Test Statistics in ABC SMC for Samples of a Bivariate Normal Random Variable -- 4 Simulation Example: Gene Expression -- 4.1 Equilibrium and Non-Equilibrium Time-Series -- 4.2 Parameter Variability -- 4.3 Tree Structure -- 5 Discussion and Outlook -- References -- Stochastic Analysis of Chemical Reaction Networks Using Linear Noise Approximation -- 1 Introduction -- 2 Chemical Reaction Networks -- 3 Linear Noise Approximation -- 3.1 Probabilistic Analysis of CRNs -- 4 Stochastic Evolution Logic (SEL) -- 4.1 LNA-based Approximate Model Checking for CRNs -- 5 Experimental Results -- 6 Concluding Remarks -- References -- Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks -- 1 Introduction -- 2 Stochastic Modeling of Biochemical Reaction Networks -- 3 Moment-Based Parameter Inference -- 4 Adaptive Approach for Parameter Inference -- 5 Case Studies -- 6 Discussion -- References -- Inferring Executable Models from Formalized Experimental Evidence -- 1 Introduction -- 2 About Pathway Logic and Datums -- 2.1 Pathway Logic -- 2.2 Datums: Formal Representation of Experimental Results -- 3 Inferring Rules from Datums: An Example -- 4 A Logical Specification for Datums -- 4.1 Assertions and Inference Rules for Datums -- 4.2 Mapping Datums to Assertions -- 5 Signaling Model of Hras Activation by Egf -- 6 Related Work and Conclusion -- References -- Symbolic Dynamics of Biochemical Pathways as Finite States Machines -- 1 Introduction -- 2 Monomolecular Networks with Totally Separated Constants. 3 Tropical Equilibrations of Nonlinear Networks with Polynomial Rate Functions -- 4 Learning a Finite State Machine from a Nonlinear Biochemical Network -- 5 Conclusion -- References -- Feature Learning Using Stacked Autoencoders to Predict the Activity of Antimicrobial Peptides -- 1 Introduction -- 2 Materials and Methods -- 2.1 Dataset and Descriptors -- 2.2 Autoencoders (AEs) -- 2.3 Stacked Autoencoder (SAE) -- 2.4 Processing Workflow -- 3 Experimental Setup -- 3.1 Experimental Configurations -- 3.2 Validation and Supervised Training -- 4 Results and Discussion -- 5 Conclusions -- References -- Structural Simplification of Chemical Reaction Networks Preserving Deterministic Semantics -- 1 Introduction -- 2 Preliminary Example -- 3 Reaction Networks -- 4 Contextual Equilibrium-Equivalence -- 5 Simplification Axioms -- 6 Simplification of the Tet-On Reaction Network -- 7 Conclusion -- References -- Automating the Development of Metabolic Network Models -- 1 Introduction -- 1.1 Adam, a Robot Scientist -- 1.2 Huginn -- 1.3 Metabolic Networks as Biological Mechanisms -- 2 Methods -- 2.1 Discovery of Mechanisms -- 2.2 Abductive Logic Programming -- 2.3 Representing Models Using Logic -- 2.4 Experiment Types and Predictions -- 2.5 Automating Crucial Tasks -- 3 Results and Conclusions -- 4 Related Work -- References -- Qualitative Reasoning for Reaction Networks with Partial Kinetic Information -- 1 Introduction -- 2 Reaction Networks -- 3 Modeling Language -- 4 Example: Regulation of Metabolism of B. subtilis -- 5 Similarity by Difference Abstraction -- 6 Abstract Interpretation to Difference Constraints -- 7 Qualitative Reasoning with Difference Constraints -- 8 Conclusion -- References -- Boolean Network Identification from Multiplex Time Series Data -- 1 Introduction -- 2 Boolean Network Identification. 2.1 Admissible Boolean Networks and Multiplex Time Series Data -- 2.2 Over-Approximation of Boolean Network Verification -- 2.3 Optimization with Respect to Time Series Data -- 2.4 Implementation -- 3 Evaluation -- 3.1 Case Study -- 3.2 Benchmarks -- 3.3 Comparison with Inferences Using Pseudo Steady-States -- 4 Conclusion -- References -- BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models -- 1 Introduction -- 2 Methods -- 3 Results -- 3.1 Personalized Prostate Cancer Treatment -- 3.2 Human Starvation -- 3.3 Cell Cycle -- 4 Conclusions and Future Work -- References -- Derivation of Qualitative Dynamical Models from Biochemical Networks -- 1 Introduction -- 2 Case Study -- 3 Trace Semantics -- 4 Derivation of a Coarse-Grained Qualitative Semantics -- 5 Refinements -- 5.1 Mass Invariants -- 5.2 Watching Interval Boundaries -- 5.3 Scales Separation -- 6 Conclusion -- References -- Model-Based Investigation of the Effect of the Cell Cycle on the Circadian Clock Through Transcription Inhibition During Mitosis -- 1 Introduction -- 2 Experimental Observations and Their Specification in Temporal Logic -- 2.1 Experimental Data -- 2.2 Temporal Logic Specification -- 3 Mathematical Models and Their Coupling -- 3.1 Model of the Cell Cycle -- 3.2 Models of the Circadian Clock -- 3.3 Coupling from the Cell Cycle to the Circadian Clock by the Inhibition of Transcription During Mitosis -- 4 Computational Results -- 4.1 Comparison to Experimental Data Without Dexamethasone -- 4.2 Comparison to Data with Dexamethasone -- 4.3 Remaining Paradox on Phase Data -- 5 Conclusion -- References -- Analysis of a Post-translational Oscillator Using Process Algebra and Spatio-Temporal Logic -- 1 Introduction -- 2 The Jolley PTO Model -- 3 Process Algebra Model Construction -- 3.1 Species -- 3.2 Interactions -- 3.3 Mixture -- 3.4 Validation. 4 Basic Time Series Analysis -- 4.1 Coupled jPTOs -- 4.2 Weaker Coupling -- 4.3 Coupling Out of Phase -- 4.4 Perturbation -- 5 Model-Checking Experiments -- 5.1 Behaviour Under Composition -- 5.2 Complex Dynamics -- 5.3 Perturbation Response -- 5.4 Results -- 6 Conclusions -- A Basic Jolley Model -- B Coupled jPTOs Model -- C Weaker Coupled jPTOs -- D Driving Other Reactions -- E Perturbation -- References -- Modeling of Resilience Properties in Oscillatory Biological Systems Using Parametric Time Petri Nets -- 1 Introduction -- 1.1 Petri Nets to Model Dynamical Biological Systems -- 1.2 Resilience Properties -- 1.3 Modeling of the Mammalian Circadian Clock -- 1.4 Our Contribution -- 1.5 Outline of the Paper -- 2 Logical Characterization of Circadian Clock Model -- 2.1 Circadian Clock Model -- 2.2 Translation of Gene Regulatory Network to Time Petri Net -- 3 Resilience of Biological Oscillatory Systems -- 3.1 Property Specification -- 3.2 Properties with Observers -- 4 Contribution and Future Work -- References -- Parameter Synthesis by Parallel Coloured CTL Model Checking -- 1 Introduction -- 2 Parallel Parameter Synthesis Algorithm -- 3 Experimental Evaluation -- 4 Conclusions -- References -- Analysing Cell Line Specific EGFR Signalling via Optimized Automata Based Model Checking -- 1 Introduction -- 2 Background -- 3 Methods -- 4 EGFR Signalling Pathway Study -- 4.1 Model Building -- 4.2 Results -- 5 Conclusion -- References -- Short Papers -- OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques -- References -- SBMLDock: Docker Driven Systems Biology Tool Development and Usage -- Abstract -- 1 Introduction -- 2 SBMLDock -- 3 Conclusion -- Acknowledgement -- References -- Author Index. |
| Record Nr. | UNISA-996466463703316 |
| Cham : , : Springer International Publishing : , : Imprint : Springer, , 2015 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
| ||
Computational Methods in Systems Biology : 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings / / edited by Olivier Roux, Jérémie Bourdon
| Computational Methods in Systems Biology : 13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings / / edited by Olivier Roux, Jérémie Bourdon |
| Edizione | [1st ed. 2015.] |
| Pubbl/distr/stampa | Cham : , : Springer International Publishing : , : Imprint : Springer, , 2015 |
| Descrizione fisica | 1 online resource (XIX, 288 p. 81 illus.) |
| Disciplina | 570.285 |
| Collana | Lecture Notes in Bioinformatics |
| Soggetto topico |
Bioinformatics
Computers Computer simulation Bioinformatics Computational biology Software engineering Computer science—Mathematics Computational Biology/Bioinformatics Computation by Abstract Devices Simulation and Modeling Computer Appl. in Life Sciences Software Engineering Symbolic and Algebraic Manipulation |
| ISBN | 3-319-23401-3 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Intro -- Preface -- Organization -- Invited Talks -- Estimation and Verification of Hybrid Heart Models for Personalised Medical and Wearable Devices -- More Thoughts on the Whole Organism Challenge -- A Genetically Modified Hoare Logic that Identifies the Parameters of a Gene Network -- Perspectives on Genome Scale Modelling of Metabolism -- Contents -- Invited Talks -- Estimation and Verification of Hybrid Heart Models for Personalised Medical and Wearable Devices -- 1 Heart Model and Personalisation -- 2 Applications and Discussion -- References -- A Genetically Modified Hoare Logic that Identifies the Parameters of a Gene Network -- 1 Thomas' Gene Regulatory Networks with Multiplexes -- 2 Hoare Triples for Gene Networks -- 3 A Hoare Logic for Gene Networks -- 4 Example -- References -- Regular Papers -- SReach: A Probabilistic Bounded Delta-Reachability Analyzer for Stochastic Hybrid Systems -- 1 Introduction -- 2 Stochastic Hybrid Models -- 3 SReach Algorithm -- 4 Experiments -- 5 Conclusions and Future Work -- References -- Experimental Design for Inference over the A. thaliana Circadian Clock Network -- 1 Introduction -- 2 Methods -- 2.1 Bayesian Experimental Design -- 2.2 Frequency-Domain Model of Gene Expression Levels -- 2.3 Experimental Design for Estimating Parameters of a DSS Model -- 2.4 A. thaliana Circadian Clock Model -- 3 Results -- 4 Conclusions -- References -- Efficient Stochastic Simulation of Systems with Multiple Time Scales via Statistical Abstraction -- 1 Introduction -- 2 Background and Related Work -- 3 Quasi-Equilibrium Reduction -- 4 Approximation of Rate Expectations -- 4.1 Continuity of Rates of the Slow System -- 4.2 Exploring Rate Expectation via Pre-simulation Runs -- 4.3 Stochastic Simulation via Statistical Abstraction -- 5 Experimental Evaluation -- 5.1 Stiff Enzyme-Substrate Reaction.
5.2 Viral Infection Model -- 6 Conclusions -- References -- Approximate Bayesian Computation for Stochastic Single-Cell Time-Lapse Data Using Multivariate Test Statistics -- 1 Introduction -- 2 Introduction to Approximate Bayesian Computation -- 3 ABC with Multivariate Test Statistics -- 3.1 Multivariate Test Statistics -- 3.2 Comparison of Test Statistics in ABC SMC for Samples of a Bivariate Normal Random Variable -- 4 Simulation Example: Gene Expression -- 4.1 Equilibrium and Non-Equilibrium Time-Series -- 4.2 Parameter Variability -- 4.3 Tree Structure -- 5 Discussion and Outlook -- References -- Stochastic Analysis of Chemical Reaction Networks Using Linear Noise Approximation -- 1 Introduction -- 2 Chemical Reaction Networks -- 3 Linear Noise Approximation -- 3.1 Probabilistic Analysis of CRNs -- 4 Stochastic Evolution Logic (SEL) -- 4.1 LNA-based Approximate Model Checking for CRNs -- 5 Experimental Results -- 6 Concluding Remarks -- References -- Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks -- 1 Introduction -- 2 Stochastic Modeling of Biochemical Reaction Networks -- 3 Moment-Based Parameter Inference -- 4 Adaptive Approach for Parameter Inference -- 5 Case Studies -- 6 Discussion -- References -- Inferring Executable Models from Formalized Experimental Evidence -- 1 Introduction -- 2 About Pathway Logic and Datums -- 2.1 Pathway Logic -- 2.2 Datums: Formal Representation of Experimental Results -- 3 Inferring Rules from Datums: An Example -- 4 A Logical Specification for Datums -- 4.1 Assertions and Inference Rules for Datums -- 4.2 Mapping Datums to Assertions -- 5 Signaling Model of Hras Activation by Egf -- 6 Related Work and Conclusion -- References -- Symbolic Dynamics of Biochemical Pathways as Finite States Machines -- 1 Introduction -- 2 Monomolecular Networks with Totally Separated Constants. 3 Tropical Equilibrations of Nonlinear Networks with Polynomial Rate Functions -- 4 Learning a Finite State Machine from a Nonlinear Biochemical Network -- 5 Conclusion -- References -- Feature Learning Using Stacked Autoencoders to Predict the Activity of Antimicrobial Peptides -- 1 Introduction -- 2 Materials and Methods -- 2.1 Dataset and Descriptors -- 2.2 Autoencoders (AEs) -- 2.3 Stacked Autoencoder (SAE) -- 2.4 Processing Workflow -- 3 Experimental Setup -- 3.1 Experimental Configurations -- 3.2 Validation and Supervised Training -- 4 Results and Discussion -- 5 Conclusions -- References -- Structural Simplification of Chemical Reaction Networks Preserving Deterministic Semantics -- 1 Introduction -- 2 Preliminary Example -- 3 Reaction Networks -- 4 Contextual Equilibrium-Equivalence -- 5 Simplification Axioms -- 6 Simplification of the Tet-On Reaction Network -- 7 Conclusion -- References -- Automating the Development of Metabolic Network Models -- 1 Introduction -- 1.1 Adam, a Robot Scientist -- 1.2 Huginn -- 1.3 Metabolic Networks as Biological Mechanisms -- 2 Methods -- 2.1 Discovery of Mechanisms -- 2.2 Abductive Logic Programming -- 2.3 Representing Models Using Logic -- 2.4 Experiment Types and Predictions -- 2.5 Automating Crucial Tasks -- 3 Results and Conclusions -- 4 Related Work -- References -- Qualitative Reasoning for Reaction Networks with Partial Kinetic Information -- 1 Introduction -- 2 Reaction Networks -- 3 Modeling Language -- 4 Example: Regulation of Metabolism of B. subtilis -- 5 Similarity by Difference Abstraction -- 6 Abstract Interpretation to Difference Constraints -- 7 Qualitative Reasoning with Difference Constraints -- 8 Conclusion -- References -- Boolean Network Identification from Multiplex Time Series Data -- 1 Introduction -- 2 Boolean Network Identification. 2.1 Admissible Boolean Networks and Multiplex Time Series Data -- 2.2 Over-Approximation of Boolean Network Verification -- 2.3 Optimization with Respect to Time Series Data -- 2.4 Implementation -- 3 Evaluation -- 3.1 Case Study -- 3.2 Benchmarks -- 3.3 Comparison with Inferences Using Pseudo Steady-States -- 4 Conclusion -- References -- BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models -- 1 Introduction -- 2 Methods -- 3 Results -- 3.1 Personalized Prostate Cancer Treatment -- 3.2 Human Starvation -- 3.3 Cell Cycle -- 4 Conclusions and Future Work -- References -- Derivation of Qualitative Dynamical Models from Biochemical Networks -- 1 Introduction -- 2 Case Study -- 3 Trace Semantics -- 4 Derivation of a Coarse-Grained Qualitative Semantics -- 5 Refinements -- 5.1 Mass Invariants -- 5.2 Watching Interval Boundaries -- 5.3 Scales Separation -- 6 Conclusion -- References -- Model-Based Investigation of the Effect of the Cell Cycle on the Circadian Clock Through Transcription Inhibition During Mitosis -- 1 Introduction -- 2 Experimental Observations and Their Specification in Temporal Logic -- 2.1 Experimental Data -- 2.2 Temporal Logic Specification -- 3 Mathematical Models and Their Coupling -- 3.1 Model of the Cell Cycle -- 3.2 Models of the Circadian Clock -- 3.3 Coupling from the Cell Cycle to the Circadian Clock by the Inhibition of Transcription During Mitosis -- 4 Computational Results -- 4.1 Comparison to Experimental Data Without Dexamethasone -- 4.2 Comparison to Data with Dexamethasone -- 4.3 Remaining Paradox on Phase Data -- 5 Conclusion -- References -- Analysis of a Post-translational Oscillator Using Process Algebra and Spatio-Temporal Logic -- 1 Introduction -- 2 The Jolley PTO Model -- 3 Process Algebra Model Construction -- 3.1 Species -- 3.2 Interactions -- 3.3 Mixture -- 3.4 Validation. 4 Basic Time Series Analysis -- 4.1 Coupled jPTOs -- 4.2 Weaker Coupling -- 4.3 Coupling Out of Phase -- 4.4 Perturbation -- 5 Model-Checking Experiments -- 5.1 Behaviour Under Composition -- 5.2 Complex Dynamics -- 5.3 Perturbation Response -- 5.4 Results -- 6 Conclusions -- A Basic Jolley Model -- B Coupled jPTOs Model -- C Weaker Coupled jPTOs -- D Driving Other Reactions -- E Perturbation -- References -- Modeling of Resilience Properties in Oscillatory Biological Systems Using Parametric Time Petri Nets -- 1 Introduction -- 1.1 Petri Nets to Model Dynamical Biological Systems -- 1.2 Resilience Properties -- 1.3 Modeling of the Mammalian Circadian Clock -- 1.4 Our Contribution -- 1.5 Outline of the Paper -- 2 Logical Characterization of Circadian Clock Model -- 2.1 Circadian Clock Model -- 2.2 Translation of Gene Regulatory Network to Time Petri Net -- 3 Resilience of Biological Oscillatory Systems -- 3.1 Property Specification -- 3.2 Properties with Observers -- 4 Contribution and Future Work -- References -- Parameter Synthesis by Parallel Coloured CTL Model Checking -- 1 Introduction -- 2 Parallel Parameter Synthesis Algorithm -- 3 Experimental Evaluation -- 4 Conclusions -- References -- Analysing Cell Line Specific EGFR Signalling via Optimized Automata Based Model Checking -- 1 Introduction -- 2 Background -- 3 Methods -- 4 EGFR Signalling Pathway Study -- 4.1 Model Building -- 4.2 Results -- 5 Conclusion -- References -- Short Papers -- OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques -- References -- SBMLDock: Docker Driven Systems Biology Tool Development and Usage -- Abstract -- 1 Introduction -- 2 SBMLDock -- 3 Conclusion -- Acknowledgement -- References -- Author Index. |
| Record Nr. | UNINA-9910484714203321 |
| Cham : , : Springer International Publishing : , : Imprint : Springer, , 2015 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||