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Symbolic Approaches to Modeling and Analysis of Biological Systems / / edited by Cedric Lhoussaine and Elisabeth Remy
| Symbolic Approaches to Modeling and Analysis of Biological Systems / / edited by Cedric Lhoussaine and Elisabeth Remy |
| Edizione | [First edition.] |
| Pubbl/distr/stampa | London, England : , : ISTE Ltd and John Wiley & Sons, Inc., , [2023] |
| Descrizione fisica | 1 online resource (397 pages) |
| Disciplina | 570.11 |
| Soggetto topico | Biological systems |
| Soggetto non controllato |
Biology
Computer Science Science Computers |
| ISBN |
1-394-22908-9
1-394-22906-2 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Cover -- Title Page -- Copyright Page -- Contents -- Preface -- Part 1. Models and Data -- Chapter 1. Inference of Gene Regulatory Networks from Multi-scale Dynamic Data -- 1.1. GRN and differentiation -- 1.1.1. The coordination of gene expression by GRNs -- 1.1.2. The process of differentiation -- 1.2. Inference of GRN from population data -- 1.2.1. Population expression data -- 1.2.2. Bayesian approaches -- 1.2.3. Information theory approaches -- 1.2.4. Boolean approaches -- 1.2.5. ODE approaches -- 1.3. Inferring GRNs from single-cell data -- 1.3.1. Single cell expression data -- 1.3.2. Adaptation of GRN inference algorithms for single-cell data analysis -- 1.3.3. Using single-cell stochastic models for GRN inference -- 1.4. Alternative strategies for GRN inference -- 1.5. Performance and limitations of GRN inference -- 1.6. Inference based on the wave of expression concept -- 1.6.1. The differentiation process seen as a dynamic process of signal processing by GRNs -- 1.6.2. Experimental demonstration of waves of expression -- 1.6.3. Using waves of expression for GRN inference -- 1.6.4. Scaling up the distributed computing approach -- 1.7. Conclusion -- 1.8. References -- Chapter 2. Combinatorial Optimization Problems for Studying Metabolism -- 2.1. Dynamics and functionality of a metabolic network -- 2.1.1. Metabolic networks -- 2.1.2. Reconstruction of metabolic networks -- 2.1.3. From the dynamics of a metabolic network to its function -- 2.2. Understanding the metabolism of non-model organisms: metabolic gap-filling algorithms -- 2.2.1. Metabolism of non-model organisms -- 2.2.2. Reconstruction of the metabolism of non-model species and gap-filling problems -- 2.2.3. Added-value and limitations of metabolic gap-filling problems: example of biotic interactions -- 2.3. Microbiota metabolism: new optimization problems.
2.3.1. Genomics of microbiota -- 2.3.2. From merged models to compartmentalized models -- 2.3.3. Completion problem for community selection in non-compartmentalized microbiota -- 2.3.4. Completion problem for selecting compartmentalized communities with minimal exchanges -- 2.4. Discrete semantics: a Boolean approximation of metabolic producibility -- 2.4.1. Topological accessibility of compounds and reactions in a metabolic network -- 2.4.2. Activation and cycles -- 2.4.3. Applications -- 2.5. Flux semantics -- 2.5.1. Modeling the response of a metabolic network with fluxes -- 2.5.2. Steady-state cycles -- 2.5.3. Application to the completion of metabolic networks -- 2.6. Comparing semantics: toward a hybrid approach -- 2.6.1. Complementarity of Boolean and stoichiometric abstractions -- 2.6.2. Hybrid completion of metabolic networks -- 2.7. Solving gap-filling problems with answer set programming -- 2.7.1. Model the Boolean activation of a reaction in ASP -- 2.7.2. Non-compartmentalized selection of communities -- 2.7.3. Compartmentalized selection of communities -- 2.8. Conclusion -- 2.9. References -- Chapter 3. The Challenges of Inferring Dynamic Models from Time Series -- 3.1. Challenges of learning about time series -- 3.2. Reconstruction of a regulation network (Boolean network) and its logical rules -- 3.2.1. Multi-valued logic -- 3.2.2. Learning operations -- 3.2.3. Dynamical semantics -- 3.2.4. GULA -- 3.2.5. PRIDE -- 3.3. Modeling Thomas networks with delays in ASP -- 3.3.1. Formalisms used -- 3.3.2. Networks -- 3.3.3. ASP technology -- 3.3.4. Description of the problem -- 3.3.5. Implementation -- 3.3.6. Results -- 3.3.7. Synthesis -- 3.4. Promise of machine learning for biology -- 3.4.1. Learning about biological regulatory networks modeling complex behaviors -- 3.4.2. Review of models -- 3.5. References. Chapter 4. Connecting Logical Models to Omics Data -- 4.1. Introduction -- 4.2. Logical models: objectives, nature and tools -- 4.2.1. Objectives and biological questions addressed -- 4.2.2. Logical modeling -- 4.2.3. Tools and resources for logical modeling -- 4.3. Building an influence graph using biological data -- 4.3.1. Defining the outline of the model -- 4.3.2. Construction of the regulation network -- 4.4. Defining logical rules and refining model parameters using biological data -- 4.4.1. Determining logical rules locally -- 4.4.2. Define or modify the logical model as a whole -- 4.5. Data to validate models and predict behaviors -- 4.6. Conclusion -- 4.7. References -- Part 2. Formal and Semantic Methods -- Chapter 5. Boolean Networks: Formalism, Semantics and Complexity -- 5.1. Introduction -- 5.2. Classical semantics of Boolean networks -- 5.2.1. Definitions -- 5.2.2. Examples -- 5.2.3. Properties -- 5.3. Related formalisms -- 5.3.1. Cellular automata -- 5.3.2. Petri nets -- 5.4. Guarantees against quantitative models -- 5.4.1. Boolean network refinements -- 5.4.2. Counterexample for classical semantics -- 5.4.3. MP Boolean networks -- 5.5. Dynamic properties and complexities -- 5.5.1. Fixed points -- 5.5.2. Reachability between configurations -- 5.5.3. Attractors -- 5.6. Conclusion -- 5.7. Acknowledgments -- 5.8. References -- Chapter 6. Computational Logic for Biomedicine and Neurosciences -- 6.1. Introduction -- 6.2. Biomedicine in linear logic -- 6.2.1. Introduction -- 6.2.2. Logical frameworks, linear logic -- 6.2.3. Modeling in LL -- 6.2.4. Modeling breast cancer progression -- 6.2.5. Verifying properties of the model -- 6.2.6. Conclusion and future perspectives on the biomedicine section -- 6.3. On the use of Coq to model and verify neuronal archetypes -- 6.3.1. Introduction -- 6.3.2. Discrete leaky integrate and fire model. 6.3.3. The basic archetypes -- 6.3.4. Modeling in Coq -- 6.3.5. Encoding neurons and archetypes in Coq -- 6.3.6. Properties of neurons and archetypes in Coq -- 6.3.7. Conclusions and future work on the archetypes section -- 6.4. Conclusion and perspective -- 6.5. References -- Chapter 7. The Cell: A Chemical Analog Calculator -- 7.1. Introduction -- 7.2. Chemical reaction networks -- 7.3. Discrete dynamics and digital calculation -- 7.4. Continuous dynamics and analog computation -- 7.5. Turing-completeness of continuous CRNs -- 7.6. Chemical compiler of calculable functions -- 7.7. Chemical programming of non-living vesicles -- 7.8. 1014 networked analog computers -- 7.9. References -- Chapter 8. Formal Verification Methods for Modeling in Biology: Biological Regulation Networks -- 8.1. Introduction -- 8.1.1. Illustrative example: the simplified circadian cycle of mammals -- 8.2. Formalization of René Thomas's modeling -- 8.2.1. Static description or influence graph -- 8.2.2. Dynamics of a biological regulation graph -- 8.3. Genetically modified Hoare logic -- 8.3.1. Using experimental observations: an example -- 8.3.2. A language of assertions -- 8.3.3. A language of paths -- 8.3.4. The power of assertions -- 8.3.5. A logic to calculate the weakest precondition -- 8.4. Temporal logic and CTL -- 8.4.1. CTL and model-checking -- 8.4.2. CTL fair path -- 8.5. TotemBioNet -- 8.5.1. Tools -- 8.5.2. Example 1: growth and apoptosis of a tadpole tail -- 8.5.3. Example 2: simplified mammalian cell cycle -- 8.6. Hybrid formalism -- 8.6.1. Hybrid regulation networks -- 8.6.2. Definition of hybrid trajectories -- 8.7. Hybrid Hoare logic -- 8.7.1. Property, path, and assertion languages -- 8.7.2. Hoare triples -- 8.7.3. Weakest precondition calculus -- 8.7.4. Inference rules -- 8.7.5. Holmes BioNet: an implementation of the processing chain. 8.8. General methodology -- 8.9. Acknowledgments -- 8.10. References -- Chapter 9. Accessible Pattern Analyses in Kappa Models -- 9.1. Introduction -- 9.1.1. Context and motivations -- 9.1.2. Modeling languages for molecular interaction systems -- 9.1.3. The Kappa language -- 9.1.4. Abstract interpretation -- 9.1.5. The Kappa ecosystem -- 9.1.6. Content of the chapter -- 9.2. Site graphs -- 9.2.1. Signature -- 9.2.2. Biochemical complexes -- 9.2.3. Patterns -- 9.2.4. Embedding between patterns -- 9.3. Rewriting site graphs -- 9.3.1. Interaction rules -- 9.3.2. Reactions induced by an interaction rule -- 9.3.3. Underlying reaction networks -- 9.4. Analysis of reachable patterns -- 9.4.1. Reachability in a reaction network -- 9.4.2. Abstraction of a set of states -- 9.4.3. Fixed point transfers -- 9.5. Analysis using sets of orthogonal patterns -- 9.5.1. Orthogonal pattern sets -- 9.5.2. Post-processing and visualization of results -- 9.5.3. Study of performance and practical use -- 9.6. Conclusion -- 9.7. References -- List of Authors -- Index -- EULA. |
| Record Nr. | UNINA-9910830486903321 |
| London, England : , : ISTE Ltd and John Wiley & Sons, Inc., , [2023] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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Synergetics : An Introduction : Nonequilibrium Phase Transitions and Self-Organization in Physics, Chemistry, and Biology / Hermann Haken
| Synergetics : An Introduction : Nonequilibrium Phase Transitions and Self-Organization in Physics, Chemistry, and Biology / Hermann Haken |
| Autore | Haken, Hermann |
| Edizione | [3. rev. and enl. ed] |
| Pubbl/distr/stampa | Berlin, : Springer, 1983 |
| Descrizione fisica | xiv, 390 p. : ill. ; 24 cm |
| Soggetto topico |
60Jxx - Markov processes [MSC 2020]
92B05 - General biology and biomathematics [MSC 2020] 58K35 - Catastrophe theory [MSC 2020] 37-XX - Dynamical systems and ergodic theory [MSC 2020] 60H10 - Stochastic ordinary differential equations [MSC 2020] 37D45 - Strange attractors, chaotic dynamics of systems with hyperbolic behavior [MSC 2020] 82-XX - Statistical mechanics, structure of matter [MSC 2020] 91B62 - Economic growth models [MSC 2020] 58E07 - Variational problems in abstract bifurcation theory in infinite-dimensional spaces [MSC 2020] 00A69 - General applied mathematics [MSC 2020] 68T05 - Learning and adaptive systems in artificial intelligence [MSC 2020] 37N20 - Dynamical systems in other branches of physics (quantum mechanics, general relativity, laser physics) [MSC 2020] 92Cxx - Physiological, cellular and medical topics [MSC 2020] 94A15 - Information theory (general) [MSC 2020] 70K50 - Bifurcations and instability for nonlinear problems in mechanics [MSC 2020] 91Dxx - Mathematical sociology (including anthropology) [MSC 2020] 82C26 - Dynamic and nonequilibrium phase transitions (general) in statistical mechanics [MSC 2020] 93C40 - Adaptive control/observation systems [MSC 2020] |
| Soggetto non controllato |
Bifurcation
Biology Chaos Diffusion Eigenvalues Entropy Equilibrium Path Integrals Phase transitions Solutions Stability Statistical Mechanics Synergetics Systems Thermodynamics |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNICAMPANIA-VAN0263063 |
Haken, Hermann
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| Berlin, : Springer, 1983 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Vanvitelli | ||
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Systems of Nonlinear Partial Differential Equations : Applications to Biology and Engineering / Anthony W. Leung
| Systems of Nonlinear Partial Differential Equations : Applications to Biology and Engineering / Anthony W. Leung |
| Autore | Leung, Anthony W. |
| Pubbl/distr/stampa | Dordrecht, : Springer, 1989 |
| Descrizione fisica | xiii, 409 p. ; 24 cm |
| Soggetto topico |
35-XX - Partial differential equations [MSC 2020]
92B05 - General biology and biomathematics [MSC 2020] 65Mxx - Numerical methods for partial differential equations, initial value and time-dependent initial-boundary value problems [MSC 2020] 65Nxx - Numerical methods for partial differential equations, boundary value problems [MSC 2020] 35J65 - Nonlinear boundary value problems for linear elliptic equations [MSC 2020] 35K57 - Reaction-diffusion equations [MSC 2020] 80A32 - Chemically reacting flows [MSC 2020] 35B32 - Bifurcation in context of PDEs [MSC 2020] 35B40 - Asymptotic behavior of solutions to PDEs [MSC 2020] |
| Soggetto non controllato |
Biology
Difference equations Differential equations Nonlinear Partial Differential Equations Partial differential equations |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNICAMPANIA-VAN0267387 |
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Leung, Anthony W.
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| Dordrecht, : Springer, 1989 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Vanvitelli | ||
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Systems Theory and Biology : Proceedings of the 3. Systems Symposium at Case Institute of Technology / M. D. Mesarović editor
| Systems Theory and Biology : Proceedings of the 3. Systems Symposium at Case Institute of Technology / M. D. Mesarović editor |
| Pubbl/distr/stampa | Berlin, : Springer, 1968 |
| Descrizione fisica | xii, 403 p. : ill. ; 24 cm |
| Soggetto topico |
92-XX - Biology and other natural sciences [MSC 2020]
93-XX - Systems theory; control [MSC 2020] |
| Soggetto non controllato |
Biology
Cybernetics Systems Theory Systems biology |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNICAMPANIA-VAN0254679 |
| Berlin, : Springer, 1968 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Vanvitelli | ||
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TEKTRAN [[electronic resource] ] : technology transfer automated retrieval system
| TEKTRAN [[electronic resource] ] : technology transfer automated retrieval system |
| Pubbl/distr/stampa | [Beltsville, Md.], : U.S. Dept. of Agriculture, Agriculture Research Service, [2000]- |
| Soggetto topico |
Agriculture - Research - United States
Nutrition - Research - United States Environmental sciences - Research - United States |
| Soggetto non controllato |
Agriculture
Biology Environment and Natural Resources Food and Nutrition |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Altri titoli varianti | TEKTRAN |
| Record Nr. | UNINA-9910691968503321 |
| [Beltsville, Md.], : U.S. Dept. of Agriculture, Agriculture Research Service, [2000]- | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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The Analysis of Categorical Data Using GLIM / James K. Lindsey
| The Analysis of Categorical Data Using GLIM / James K. Lindsey |
| Autore | Lindsey, James K. |
| Pubbl/distr/stampa | New York, : Springer-Verlag, 1989 |
| Descrizione fisica | v, 168 p. : ill. ; 24 cm |
| Soggetto topico | 62-XX - Statistics [MSC 2020] |
| Soggetto non controllato |
Biology
Economics Markov Chains Odds Population Statistics |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNICAMPANIA-VAN0269241 |
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Lindsey, James K.
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| New York, : Springer-Verlag, 1989 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Vanvitelli | ||
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Thermodynamic Network Analysis of Biological Systems / J. Schnakenberg
| Thermodynamic Network Analysis of Biological Systems / J. Schnakenberg |
| Autore | Schnakenberg, Jürgen |
| Edizione | [2. corr. and Up. ed] |
| Pubbl/distr/stampa | Berlin, : Springer, 1981 |
| Descrizione fisica | x, 150 p. : ill. ; 24 cm |
| Soggetto topico |
92B05 - General biology and biomathematics [MSC 2020]
92-XX - Biology and other natural sciences [MSC 2020] 80-XX - Classical thermodynamics, heat transfer [MSC 2020] 94C05 - Analytic circuit theory [MSC 2020] 92Cxx - Physiological, cellular and medical topics [MSC 2020] 92Exx - Chemistry [MSC 2020] 94C15 - Applications of graph theory to circuits and networks [MSC 2020] |
| Soggetto non controllato |
Analysis
Biological mathematical models Biology Life Sciences Networks Physical concepts Physiology Thermodynamics |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNICAMPANIA-VAN0261911 |
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Schnakenberg, Jürgen
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| Berlin, : Springer, 1981 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Vanvitelli | ||
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Thermodynamic Network Analysis of Biological Systems / J. Schnakenberg
| Thermodynamic Network Analysis of Biological Systems / J. Schnakenberg |
| Autore | Schnakenberg, Jürgen |
| Pubbl/distr/stampa | Berlin, : Springer, 1977 |
| Descrizione fisica | viii, 143 p. : ill. ; 24 cm |
| Soggetto topico |
92B05 - General biology and biomathematics [MSC 2020]
91B06 - Decision theory [MSC 2020] |
| Soggetto non controllato |
Analysis
Biological mathematical models Biology Life Sciences Networks Physical concepts Physiology Thermodynamics |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNICAMPANIA-VAN0260513 |
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Schnakenberg, Jürgen
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| Berlin, : Springer, 1977 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Vanvitelli | ||
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Three Concepts of Time / Kenneth G. Denbigh
| Three Concepts of Time / Kenneth G. Denbigh |
| Autore | Denbigh, Kenneth G. |
| Pubbl/distr/stampa | Berlin, : Springer, 1981 |
| Descrizione fisica | viii, 180 p. : ill. ; 24 cm |
| Soggetto topico |
00A79 (77-XX) - Physics [MSC 2020]
00-XX - General and overarching topics; collections [MSC 2020] 00Axx - General and miscellaneous specific topics [MSC 2020] |
| Soggetto non controllato |
Biology
Causality Entropy Invariants Objectivity Time |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNICAMPANIA-VAN0261912 |
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Denbigh, Kenneth G.
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| Berlin, : Springer, 1981 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Vanvitelli | ||
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Vermi con ali di farfalla : l'evoluzione come idea filosofica / / Luigi Bianchi
| Vermi con ali di farfalla : l'evoluzione come idea filosofica / / Luigi Bianchi |
| Autore | Bianchi Luigi <1923-> |
| Edizione | [1. ed.] |
| Pubbl/distr/stampa | Roma, : Viella, 2012 |
| Descrizione fisica | 178 p. ; ; 21 cm |
| Collana | La storia. Temi |
| Soggetto topico | Evolution (Biology) - Philosophy |
| Soggetto non controllato |
Biology
Science |
| ISBN | 88-6728-190-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | ita |
| Altri titoli varianti | Vermi con ali di farfalla |
| Record Nr. | UNINA-9910135353903321 |
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Bianchi Luigi <1923->
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| Roma, : Viella, 2012 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
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