Computer Programming In Quantitative Biology
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Computer Programming In Quantitative Biology
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Author : R.G. Davies
language : en
Publisher: Elsevier
Release Date : 2012-12-02
Computer Programming In Quantitative Biology written by R.G. Davies and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-12-02 with Reference categories.
Computer Programming in Quantitative Biology covers the general background of Fortran coding and the more sophisticated computer programs likely to be encountered in quantitative biology. It discusses the application of over 40 appropriate and easily adaptable programming techniques to problems of major biological interest. Organized into 15 chapters, the book starts by providing an introductory outline of computer structure and function needed to appreciate many basic programming procedures. A chapter discusses some general principles underlying Fortran coding and the use of digital computers, with emphasis on major features of Fortran IV. Other chapters present short introduction to the statistical or mathematical techniques in each of the main sections under which program are described. These chapters also provide some aspects of matrix algebra that are essential for serious statistical programming and offer a general guide to efficiency in programming. All complete programs are accompanied by a flowchart and a detailed discussion. This book is a valuable source of information for biologists, computational biologists, research biologists, undergraduate students, and advanced or specialized students of biology.
Quantitative Biology
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Author : Brian Munsky
language : en
Publisher: MIT Press
Release Date : 2018-08-21
Quantitative Biology written by Brian Munsky and has been published by MIT Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-08-21 with Science categories.
An introduction to the quantitative modeling of biological processes, presenting modeling approaches, methodology, practical algorithms, software tools, and examples of current research. The quantitative modeling of biological processes promises to expand biological research from a science of observation and discovery to one of rigorous prediction and quantitative analysis. The rapidly growing field of quantitative biology seeks to use biology's emerging technological and computational capabilities to model biological processes. This textbook offers an introduction to the theory, methods, and tools of quantitative biology. The book first introduces the foundations of biological modeling, focusing on some of the most widely used formalisms. It then presents essential methodology for model-guided analyses of biological data, covering such methods as network reconstruction, uncertainty quantification, and experimental design; practical algorithms and software packages for modeling biological systems; and specific examples of current quantitative biology research and related specialized methods. Most chapters offer problems, progressing from simple to complex, that test the reader's mastery of such key techniques as deterministic and stochastic simulations and data analysis. Many chapters include snippets of code that can be used to recreate analyses and generate figures related to the text. Examples are presented in the three popular computing languages: Matlab, R, and Python. A variety of online resources supplement the the text. The editors are long-time organizers of the Annual q-bio Summer School, which was founded in 2007. Through the school, the editors have helped to train more than 400 visiting students in Los Alamos, NM, Santa Fe, NM, San Diego, CA, Albuquerque, NM, and Fort Collins, CO. This book is inspired by the school's curricula, and most of the contributors have participated in the school as students, lecturers, or both. Contributors John H. Abel, Roberto Bertolusso, Daniela Besozzi, Michael L. Blinov, Clive G. Bowsher, Fiona A. Chandra, Paolo Cazzaniga, Bryan C. Daniels, Bernie J. Daigle, Jr., Maciej Dobrzynski, Jonathan P. Doye, Brian Drawert, Sean Fancer, Gareth W. Fearnley, Dirk Fey, Zachary Fox, Ramon Grima, Andreas Hellander, Stefan Hellander, David Hofmann, Damian Hernandez, William S. Hlavacek, Jianjun Huang, Tomasz Jetka, Dongya Jia, Mohit Kumar Jolly, Boris N. Kholodenko, Markek Kimmel, Michał Komorowski, Ganhui Lan, Heeseob Lee, Herbert Levine, Leslie M Loew, Jason G. Lomnitz, Ard A. Louis, Grant Lythe, Carmen Molina-París, Ion I. Moraru, Andrew Mugler, Brian Munsky, Joe Natale, Ilya Nemenman, Karol Nienałtowski, Marco S. Nobile, Maria Nowicka, Sarah Olson, Alan S. Perelson, Linda R. Petzold, Sreenivasan Ponnambalam, Arya Pourzanjani, Ruy M. Ribeiro, William Raymond, William Raymond, Herbert M. Sauro, Michael A. Savageau, Abhyudai Singh, James C. Schaff, Boris M. Slepchenko, Thomas R. Sokolowski, Petr Šulc, Andrea Tangherloni, Pieter Rein ten Wolde, Philipp Thomas, Karen Tkach Tuzman, Lev S. Tsimring, Dan Vasilescu, Margaritis Voliotis, Lisa Weber
Quantitative Biology
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Author : Akatsuki Kimura
language : en
Publisher: Springer Nature
Release Date : 2022-01-04
Quantitative Biology written by Akatsuki Kimura and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-01-04 with Science categories.
This textbook is for biologists, to conduct quantitative analysis and modeling of biological processes at molecular and cellular levels. Focusing on practical concepts and techniques for everyday research, this text will enable beginners, both students and established biologists, to take the first step in quantitative biology. It also provides step-by-step tutorials to run various sample programs in one’s personal computer using Excel and Python. This volume traces topics, starting with an introductory chapter, such as modeling, construction and execution of numerical models, and key concepts in quantitative biology: feedback regulations, fluctuations and randomness, and statistical analyses. It also provide sample codes with guidance to procedure programming for actual biological processes such as movement of the nucleus within a cell, cell-cycle regulation, stripe pattern formation of skins, and distribution of energy. Written by a leading research scientist who has a background in biology, studied quantitative approaches by himself, and teaches quantitative biology at several universities, this textbook broadens quantitative approaches for biologists who do not have a strong background in mathematics, physics, or computer programming, and helps them progress further in their research.
Integer Linear Programming In Computational And Systems Biology
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Author : Dan Gusfield
language : en
Publisher: Cambridge University Press
Release Date : 2019-06-13
Integer Linear Programming In Computational And Systems Biology written by Dan Gusfield and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-06-13 with Computers categories.
This hands-on tutorial text for non-experts demonstrates biological applications of a versatile modeling and optimization technique.
Foundations Of Theoretical Approaches In Systems Biology
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Author : Alberto Marin-Sanguino
language : en
Publisher: Frontiers Media SA
Release Date : 2019-01-11
Foundations Of Theoretical Approaches In Systems Biology written by Alberto Marin-Sanguino and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-01-11 with categories.
If biology in the 20th century was characterized by an explosion of new technologies and experimental methods, that of the 21st has seen an equally exuberant proliferation of mathematical and computational methods that attempt to systematize and explain the abundance of available data. As we live through the consolidation of a new paradigm where experimental data goes hand in hand with computational analysis, we contemplate the challenge of fusing these two aspects of the new biology into a consistent theoretical framework. Whether systems biology will survive as a field or be washed away by the tides of future fads will ultimately depend on its success to achieve this type of synthesis. The famous quote attributed to Kurt Lewin comes to mind: "there is nothing more practical than a good theory". This book presents a wide assortment of articles on systems biology in an attempt to capture the variety of current methods in systems biology and show how they can help to find answers to the challenges of modern biology.
Parallel Computing For Bioinformatics And Computational Biology
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Author : Albert Y. Zomaya
language : en
Publisher: John Wiley & Sons
Release Date : 2006-04-14
Parallel Computing For Bioinformatics And Computational Biology written by Albert Y. Zomaya and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-04-14 with Computers categories.
Discover how to streamline complex bioinformatics applications with parallel computing This publication enables readers to handle more complex bioinformatics applications and larger and richer data sets. As the editor clearly shows, using powerful parallel computing tools can lead to significant breakthroughs in deciphering genomes, understanding genetic disease, designing customized drug therapies, and understanding evolution. A broad range of bioinformatics applications is covered with demonstrations on how each one can be parallelized to improve performance and gain faster rates of computation. Current parallel computing techniques and technologies are examined, including distributed computing and grid computing. Readers are provided with a mixture of algorithms, experiments, and simulations that provide not only qualitative but also quantitative insights into the dynamic field of bioinformatics. Parallel Computing for Bioinformatics and Computational Biology is a contributed work that serves as a repository of case studies, collectively demonstrating how parallel computing streamlines difficult problems in bioinformatics and produces better results. Each of the chapters is authored by an established expert in the field and carefully edited to ensure a consistent approach and high standard throughout the publication. The work is organized into five parts: * Algorithms and models * Sequence analysis and microarrays * Phylogenetics * Protein folding * Platforms and enabling technologies Researchers, educators, and students in the field of bioinformatics will discover how high-performance computing can enable them to handle more complex data sets, gain deeper insights, and make new discoveries.
Handbook Of Research On Systems Biology Applications In Medicine
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Author : Daskalaki, Andriani
language : en
Publisher: IGI Global
Release Date : 2008-11-30
Handbook Of Research On Systems Biology Applications In Medicine written by Daskalaki, Andriani and has been published by IGI Global this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-11-30 with Technology & Engineering categories.
"This book highlights the use of systems approaches including genomic, cellular, proteomic, metabolomic, bioinformatics, molecular, and biochemical, to address fundamental questions in complex diseases like cancer diabetes but also in ageing"--Provided by publisher.
Bioinformatics And Computational Biology
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Author : Basant K. Tiwary
language : en
Publisher: Springer Nature
Release Date : 2021-11-23
Bioinformatics And Computational Biology written by Basant K. Tiwary and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-11-23 with Medical categories.
This textbook introduces fundamental concepts of bioinformatics and computational biology to the students and researchers in biology, medicine, veterinary science, agriculture, and bioengineering . The respective chapters provide detailed information on biological databases, sequence alignment, molecular evolution, next-generation sequencing, systems biology, and statistical computing using R. The book also presents a case-based discussion on clinical, veterinary, agricultural bioinformatics, and computational bioengineering for application-based learning in the respective fields. Further, it offers readers guidance on reconstructing and analysing biological networks and highlights computational methods used in systems medicine and genome-wide association mapping of diseases. Given its scope, this textbook offers an essential introductory book on bioinformatics and computational biology for undergraduate and graduate students in the life sciences, botany, zoology, physiology, biotechnology, bioinformatics, and genomic science as well as systems biology, bioengineering and the agricultural, and veterinary sciences.
An Introduction To Computational Systems Biology
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Author : Karthik Raman
language : en
Publisher: CRC Press
Release Date : 2021-05-30
An Introduction To Computational Systems Biology written by Karthik Raman and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-05-30 with Computers categories.
This book delivers a comprehensive and insightful account of applying mathematical modelling approaches to very large biological systems and networks—a fundamental aspect of computational systems biology. The book covers key modelling paradigms in detail, while at the same time retaining a simplicity that will appeal to those from less quantitative fields. Key Features: A hands-on approach to modelling Covers a broad spectrum of modelling, from static networks to dynamic models and constraint-based models Thoughtful exercises to test and enable understanding of concepts State-of-the-art chapters on exciting new developments, like community modelling and biological circuit design Emphasis on coding and software tools for systems biology Companion website featuring lecture videos, figure slides, codes, supplementary exercises, further reading, and appendices: https://ramanlab.github.io/SysBioBook/ An Introduction to Computational Systems Biology: Systems-Level Modelling of Cellular Networks is highly multi-disciplinary and will appeal to biologists, engineers, computer scientists, mathematicians and others.
Computational Methods In Systems Biology
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Author : Pierpaolo Degano
language : en
Publisher: Springer
Release Date : 2009-08-27
Computational Methods In Systems Biology written by Pierpaolo Degano and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-08-27 with Science categories.
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.