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Optimization Models And Computational Methods For Systems Biology
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Book Synopsis Biological Modeling and Simulation by : Russell Schwartz
Download or read book Biological Modeling and Simulation written by Russell Schwartz and published by MIT Press. This book was released on 2008-07-25 with total page 403 pages. Available in PDF, EPUB and Kindle. Book excerpt: A practice-oriented survey of techniques for computational modeling and simulation suitable for a broad range of biological problems. There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis. It collects in one place a selection of broadly useful models, algorithms, and theoretical analysis tools normally found scattered among many other disciplines. It thereby gives the aspiring student a bag of tricks that will serve him or her well in modeling problems drawn from numerous subfields of biology. These techniques are taught from the perspective of what the practitioner needs to know to use them effectively, supplemented with references for further reading on more advanced use of each method covered. The text, which grew out of a class taught at Carnegie Mellon University, covers models for optimization, simulation and sampling, and parameter tuning. These topics provide a general framework for learning how to formulate mathematical models of biological systems, what techniques are available to work with these models, and how to fit the models to particular systems. Their application is illustrated by many examples drawn from a variety of biological disciplines and several extended case studies that show how the methods described have been applied to real problems in biology.
Book Synopsis Methods in Computational Biology by : Ross Carlson
Download or read book Methods in Computational Biology written by Ross Carlson and published by MDPI. This book was released on 2019-07-03 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern biology is rapidly becoming a study of large sets of data. Understanding these data sets is a major challenge for most life sciences, including the medical, environmental, and bioprocess fields. Computational biology approaches are essential for leveraging this ongoing revolution in omics data. A primary goal of this Special Issue, entitled “Methods in Computational Biology”, is the communication of computational biology methods, which can extract biological design principles from complex data sets, described in enough detail to permit the reproduction of the results. This issue integrates interdisciplinary researchers such as biologists, computer scientists, engineers, and mathematicians to advance biological systems analysis. The Special Issue contains the following sections: • Reviews of Computational Methods • Computational Analysis of Biological Dynamics: From Molecular to Cellular to Tissue/Consortia Levels • The Interface of Biotic and Abiotic Processes • Processing of Large Data Sets for Enhanced Analysis • Parameter Optimization and Measurement
Book Synopsis Integer Linear Programming in Computational and Systems Biology by : Dan Gusfield
Download or read book Integer Linear Programming in Computational and Systems Biology written by Dan Gusfield and published by Cambridge University Press. This book was released on 2019-06-13 with total page 431 pages. Available in PDF, EPUB and Kindle. Book excerpt: This hands-on tutorial text for non-experts demonstrates biological applications of a versatile modeling and optimization technique.
Book Synopsis Computational Methods for Estimating the Kinetic Parameters of Biological Systems by : Quentin Vanhaelen
Download or read book Computational Methods for Estimating the Kinetic Parameters of Biological Systems written by Quentin Vanhaelen and published by Humana. This book was released on 2022-12-24 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed book provides an overview of various classes of computational techniques, including machine learning techniques, commonly used for evaluating kinetic parameters of biological systems. Focusing on three distinct situations, the volume covers the prediction of the kinetics of enzymatic reactions, the prediction of the kinetics of protein-protein or protein-ligand interactions (binding rates, dissociation rates, binding affinities), and the prediction of relatively large set of kinetic rates of reactions usually found in quantitative models of large biological networks. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of expert implementation advice that leads to successful results. Authoritative and practical, Computational Methods for Estimating the Kinetic Parameters of Biological Systems will be of great interest for researchers working through the challenge of identifying the best type of algorithm and who would like to use or develop a computational method for the estimation of kinetic parameters.
Book Synopsis Computational Methods in Systems Biology by : Pedro Mendes
Download or read book Computational Methods in Systems Biology written by Pedro Mendes and published by Springer. This book was released on 2014-10-20 with total page 279 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the 12th International Conference on Computational Methods in Systems Biology, CMSB 2014, held in Manchester, UK, in November 2014. The 16 regular papers presented together with 6 poster papers were carefully reviewed and selected from 31 regular and 18 poster submissions. The papers are organized in topical sections on formalisms for modeling biological processes, model inference from experimental data, frameworks for model verification, validation, and analysis of biological systems, models and their biological applications, computational approaches for synthetic biology, and flash posters.
Book Synopsis Computational Methods in Systems Biology by : Ezio Bartocci
Download or read book Computational Methods in Systems Biology written by Ezio Bartocci and published by Springer. This book was released on 2016-09-03 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 14th International Conference on Computational Methods in Systems Biology, CMSB 2016, held in Cambridge, UK, in September 2016. The 20 full papers, 3 tool papers and 9 posters presented were carefully reviewed and selected from 37 regular paper submissions. The topics 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; and computational approaches for synthetic biology.
Book Synopsis Computational Methods in Systems Biology by : David Gilbert
Download or read book Computational Methods in Systems Biology written by David Gilbert and published by Springer. This book was released on 2012-09-28 with total page 404 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the thoroughly refereed conference proceedings of the 10th International Conference on Computational Methods in Systems Biology, CMSB 2012, held in London, UK, during October 3-5, 2012. The 17 revised full papers and 8 flash posters presented together with the summaries of 3 invited papers were carefully reviewed and selected from 62 submissions. The papers cover the analysis of biological systems, networks, and data ranging from intercellular to multiscale. Topics included high-performance computing, and for the first time papers on synthetic biology.
Book Synopsis Computational Methods in Systems Biology by : Monika Heiner
Download or read book Computational Methods in Systems Biology written by Monika Heiner and published by Springer Science & Business Media. This book was released on 2008-10-07 with total page 413 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 6th International Conference on Computational Methods in Systems Biology, CMSB 2008, held in Rostock, Germany, in September 2008. The 21 revised full papers presented together with the summaries of 5 invited papers were carefully reviewed and selected from more than 60 submissions. The papers cover theoretical or applied contributions that are motivated by a biological question focusing on modeling approaches, including process algebra, simulation approaches, analysis methods, in particular model checking and flux analysis, and case studies.
Book Synopsis Computational Methods in Systems Biology by : Pierpaolo Degano
Download or read book Computational Methods in Systems Biology written by Pierpaolo Degano and published by Springer. This book was released on 2009-08-27 with total page 337 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains the proceedings of the 7th Conference on Computational Methods in Systems Biology (CMSB 2009), held in Bologna, from August 31 to September 1, 2009. The ?rst CMSB was held in Trento in 2003, bringing together life scientists, computer scientists, engineers and physicists. The goal was to promote the c- vergence of di?erent disciplines aiming at a new understanding and description of biological systems, ?rmly ground in formal models, supported by compu- tionallanguagesandtools,ando?eringnew methodsofanalysis.The conference then moved to Paris in 2004, Edinburgh in 2005, Trento in 2006, Edinburgh in 2007 and Rostock/Warnemunde ̈ in 2008. This year the conference attracted about 45 submissions form 18 countries, mainly from Europe and North America, but also from Asia and Australia. We wish to thank all authors for their interest in CMSB 2009. After careful disc- sions, the Programme Committee eventually selected 18 papers for presentation at the conference. Each of them was accurately refereed by at least three - viewers, who delivered detailed and insightful comments and suggestions. The Conference Chairmen warmly thank all the members of the Programme C- mittee and all their sub-referees for the excellent support they gave, as well as for the friendly and constructive discussions. We also would like to thank the authorsfor havingrevisedtheir papers to addressthe comments andsuggestions by the referees.
Book Synopsis A Course in Mathematical Biology by : Gerda de Vries
Download or read book A Course in Mathematical Biology written by Gerda de Vries and published by SIAM. This book was released on 2006-07-01 with total page 307 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the only book that teaches all aspects of modern mathematical modeling and that is specifically designed to introduce undergraduate students to problem solving in the context of biology. Included is an integrated package of theoretical modeling and analysis tools, computational modeling techniques, and parameter estimation and model validation methods, with a focus on integrating analytical and computational tools in the modeling of biological processes. Divided into three parts, it covers basic analytical modeling techniques; introduces computational tools used in the modeling of biological problems; and includes various problems from epidemiology, ecology, and physiology. All chapters include realistic biological examples, including many exercises related to biological questions. In addition, 25 open-ended research projects are provided, suitable for students. An accompanying Web site contains solutions and a tutorial for the implementation of the computational modeling techniques. Calculations can be done in modern computing languages such as Maple, Mathematica, and MATLAB?.
Book Synopsis Computational Methods in Systems Biology by : Milan Češka
Download or read book Computational Methods in Systems Biology written by Milan Češka and published by Springer. This book was released on 2018-08-27 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 16th International Conference on Computational Methods in Systems Biology, CMSB 2018, held in BRNO, Czech Republic, in September 2018. The 15 full and 7 short papers presented together with 5 invited talks were carefully reviewed and selected from 46 submissions. 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; parameter and model inference from experimental data; automated parameter and model synthesis; model integration and biological databases; multi-scale modeling and analysis methods; design, analysis, and verification methods for synthetic biology; methods for biomolecular computing and engineered molecular devices. Chapters 3, 9 and 10 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Book Synopsis Computational Methods in Systems Biology by : Eugenio Cinquemani
Download or read book Computational Methods in Systems Biology written by Eugenio Cinquemani and published by Springer Nature. This book was released on 2021-09-13 with total page 292 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 19th International Conference on Computational Methods in Systems Biology, CMSB 2021, held in Bordeaux, France, September 22–24, 2021.*The 13 full papers and 5 tool papers were carefully reviewed and selected from 32 submissions. The topics of interest include biological process modelling; biological system model verification, validation, analysis, and simulation; high-performance computational systems biology; model inference from experimental data; multi-scale modeling and analysis methods; computational approaches for synthetic biology; machine learning and data-driven approaches; microbial ecology modelling and analysis; methods and protocols for populations and their variability; models, applications, and case studies in systems and synthetic biology. The chapters "Microbial Community Decision Making Models in Batch", "Population design for synthetic gene circuits", "BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems" are published open access under a CC BY license (Creative Commons Attribution 4.0 International License). * The conference was held in a hybrid mode due to the COVID-19 pandemic.
Book Synopsis Computational Methods in Systems Biology by : Alessandro Abate
Download or read book Computational Methods in Systems Biology written by Alessandro Abate and published by Springer Nature. This book was released on 2020-10-01 with total page 397 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Computational Methods in Systems Biology by : Roberta Gori
Download or read book Computational Methods in Systems Biology written by Roberta Gori and published by Springer Nature. This book was released on with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Computational Methods in Systems Biology by : Jun Pang
Download or read book Computational Methods in Systems Biology written by Jun Pang and published by Springer Nature. This book was released on with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Computational Methods in Systems Biology by : Ashutosh Gupta
Download or read book Computational Methods in Systems Biology written by Ashutosh Gupta and published by Springer. This book was released on 2013-09-18 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the 11th International Conference on Computational Methods in Systems Biology, CMSB 2013, held in Klosterneuburg, Austria, in September 2013. The 15 regular papers included in this volume were carefully reviewed and selected from 27 submissions. They deal with computational models for all levels, from molecular and cellular, to organs and entire organisms.
Book Synopsis Computational Methods in Systems Biology by : Luca Bortolussi
Download or read book Computational Methods in Systems Biology written by Luca Bortolussi and published by Springer Nature. This book was released on 2019-09-16 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 17th International Conference on Computational Methods in Systems Biology, CMSB 2019, held in Trieste, Italy, in September 2019. The 14 full papers, 7 tool papers and 11 posters were carefully reviewed and selected from 53 submissions. 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.
