A Primer For Computational Biology

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A Primer for Computational Biology

Author : Shawn T. O'Neil
Publisher :
ISBN 13 : 9780870719264
Total Pages : 0 pages
Book Rating : 4.7/5 (192 download)

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Book Synopsis A Primer for Computational Biology by : Shawn T. O'Neil

Download or read book A Primer for Computational Biology written by Shawn T. O'Neil and published by . This book was released on 2017-12-21 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: A Primer for Computational Biology aims to provide life scientists and students the skills necessary for research in a data-rich world. The text covers accessing and using remote servers via the command-line, writing programs and pipelines for data analysis, and provides useful vocabulary for interdisciplinary work. The book is broken into three parts: Introduction to Unix/Linux: The command-line is the "natural environment" of scientific computing, and this part covers a wide range of topics, including logging in, working with files and directories, installing programs and writing scripts, and the powerful "pipe" operator for file and data manipulation. Programming in Python: Python is both a premier language for learning and a common choice in scientific software development. This part covers the basic concepts in programming (data types, if-statements and loops, functions) via examples of DNA-sequence analysis. This part also covers more complex subjects in software development such as objects and classes, modules, and APIs. Programming in R: The R language specializes in statistical data analysis, and is also quite useful for visualizing large datasets. This third part covers the basics of R as a programming language (data types, if-statements, functions, loops and when to use them) as well as techniques for large-scale, multi-test analyses. Other topics include S3 classes and data visualization with ggplot2.

Bioinformatics and Computational Biology

Author : Basant K. Tiwary
Publisher : Springer Nature
ISBN 13 : 9811642419
Total Pages : 239 pages
Book Rating : 4.8/5 (116 download)

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Book Synopsis Bioinformatics and Computational Biology by : Basant K. Tiwary

Download or read book Bioinformatics and Computational Biology written by Basant K. Tiwary and published by Springer Nature. This book was released on 2021-11-23 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Computational Modeling of Genetic and Biochemical Networks

Author : James M. Bower
Publisher : MIT Press
ISBN 13 : 9780262524230
Total Pages : 386 pages
Book Rating : 4.5/5 (242 download)

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Book Synopsis Computational Modeling of Genetic and Biochemical Networks by : James M. Bower

Download or read book Computational Modeling of Genetic and Biochemical Networks written by James M. Bower and published by MIT Press. This book was released on 2001 with total page 386 pages. Available in PDF, EPUB and Kindle. Book excerpt: How new modeling techniques can be used to explore functionally relevant molecular and cellular relationships.

Computational Biology

Author : Scott T. Kelley
Publisher : John Wiley & Sons
ISBN 13 : 1683673034
Total Pages : 181 pages
Book Rating : 4.6/5 (836 download)

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Book Synopsis Computational Biology by : Scott T. Kelley

Download or read book Computational Biology written by Scott T. Kelley and published by John Wiley & Sons. This book was released on 2018-01-01 with total page 181 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook is for anyone who needs to learn the basics of bioinformatics—the use of computational methods to better understand biological systems. Computational Biology covers the principles and applications of the computational methods used to study DNA, RNA, and proteins, including using biological databases such as NCBI and UniProt; performing BLAST, sequence alignments, and structural predictions; and creating phylogenetic trees. It includes a primer that can be used as a jumping off point for learning computer programming for bioinformatics. This text can be used as a self-study guide, as a course focused on computational methods in biology/bioinformatics, or to supplement general courses that touch on topics included within the book. Computational Biology's robust interactive online components “gamify” the study of bioinformatics, allowing the reader to practice randomly generated problems on their own time to build confidence and skill and gain practical real-world experience. The online component also assures that the content being taught is up to date and accurately reflects the ever-changing landscape of bioinformatics web-based programs.

An Introduction to Systems Biology

Author : Uri Alon
Publisher : CRC Press
ISBN 13 : 1584886420
Total Pages : 324 pages
Book Rating : 4.5/5 (848 download)

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Book Synopsis An Introduction to Systems Biology by : Uri Alon

Download or read book An Introduction to Systems Biology written by Uri Alon and published by CRC Press. This book was released on 2006-07-07 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The textavoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles. An Introduction to Systems Biology: Design Principles of Biological Circuits builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.

A Primer on Scientific Programming with Python

Author : Hans Petter Langtangen
Publisher : Springer
ISBN 13 : 3662498871
Total Pages : 942 pages
Book Rating : 4.6/5 (624 download)

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Book Synopsis A Primer on Scientific Programming with Python by : Hans Petter Langtangen

Download or read book A Primer on Scientific Programming with Python written by Hans Petter Langtangen and published by Springer. This book was released on 2016-07-28 with total page 942 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book serves as a first introduction to computer programming of scientific applications, using the high-level Python language. The exposition is example and problem-oriented, where the applications are taken from mathematics, numerical calculus, statistics, physics, biology and finance. The book teaches "Matlab-style" and procedural programming as well as object-oriented programming. High school mathematics is a required background and it is advantageous to study classical and numerical one-variable calculus in parallel with reading this book. Besides learning how to program computers, the reader will also learn how to solve mathematical problems, arising in various branches of science and engineering, with the aid of numerical methods and programming. By blending programming, mathematics and scientific applications, the book lays a solid foundation for practicing computational science. From the reviews: Langtangen ... does an excellent job of introducing programming as a set of skills in problem solving. He guides the reader into thinking properly about producing program logic and data structures for modeling real-world problems using objects and functions and embracing the object-oriented paradigm. ... Summing Up: Highly recommended. F. H. Wild III, Choice, Vol. 47 (8), April 2010 Those of us who have learned scientific programming in Python ‘on the streets’ could be a little jealous of students who have the opportunity to take a course out of Langtangen’s Primer.” John D. Cook, The Mathematical Association of America, September 2011 This book goes through Python in particular, and programming in general, via tasks that scientists will likely perform. It contains valuable information for students new to scientific computing and would be the perfect bridge between an introduction to programming and an advanced course on numerical methods or computational science. Alex Small, IEEE, CiSE Vol. 14 (2), March /April 2012 “This fourth edition is a wonderful, inclusive textbook that covers pretty much everything one needs to know to go from zero to fairly sophisticated scientific programming in Python...” Joan Horvath, Computing Reviews, March 2015

An Introduction to Computational Systems Biology

Author : Karthik Raman
Publisher : CRC Press
ISBN 13 : 0429944527
Total Pages : 359 pages
Book Rating : 4.4/5 (299 download)

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Book Synopsis An Introduction to Computational Systems Biology by : Karthik Raman

Download or read book An Introduction to Computational Systems Biology written by Karthik Raman and published by CRC Press. This book was released on 2021-05-30 with total page 359 pages. Available in PDF, EPUB and Kindle. Book excerpt: Emphasises a hands-on approach to modelling Strong emphasis on coding and software tools for systems biology Covers the entire spectrum of modelling, from static networks, to dynamic models Thoughtful exercises to test and enable student understanding of concepts Current chapters on exciting new developments like whole-cell modelling and community modelling

Practical Applications of Computational Biology and Bioinformatics, 13th International Conference

Author : Florentino Fdez-Riverola
Publisher : Springer
ISBN 13 : 3030238733
Total Pages : 184 pages
Book Rating : 4.0/5 (32 download)

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Book Synopsis Practical Applications of Computational Biology and Bioinformatics, 13th International Conference by : Florentino Fdez-Riverola

Download or read book Practical Applications of Computational Biology and Bioinformatics, 13th International Conference written by Florentino Fdez-Riverola and published by Springer. This book was released on 2019-06-21 with total page 184 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book features 21 papers spanning many different sub-fields in bioinformatics and computational biology, presenting the latest research on the practical applications to promote fruitful interactions between young researchers in different areas related to the field. Next-generation sequencing technologies, together with other emerging and diverse experimental techniques, are evolving rapidly, creating numerous types of omics data. These, in turn, are creating new challenges for the expanding fields of bioinformatics and computational biology, which seek to analyse, process, integrate and extract meaningful knowledge from such data. This calls for new algorithms and approaches from fields such as databases, statistics, data mining, machine learning, optimization, computer science, machine learning and artificial intelligence. Clearly, biology is increasingly becoming a science of information, requiring tools from the computational sciences. To address these challenges, we have seen the emergence of a new generation of interdisciplinary scientists with a strong background in the biological and computational sciences. In this context, the interaction of researchers from different scientific areas is, more than ever, vital to boost the research efforts in the field and contribute to the training of the new generation of interdisciplinary scientists.

Kernel Methods in Computational Biology

Author : Bernhard Schölkopf
Publisher : MIT Press
ISBN 13 : 9780262195096
Total Pages : 428 pages
Book Rating : 4.1/5 (95 download)

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Book Synopsis Kernel Methods in Computational Biology by : Bernhard Schölkopf

Download or read book Kernel Methods in Computational Biology written by Bernhard Schölkopf and published by MIT Press. This book was released on 2004 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: A detailed overview of current research in kernel methods and their application to computational biology.

Cellular Biophysics and Modeling

Author : Greg Conradi Smith
Publisher : Cambridge University Press
ISBN 13 : 1107005361
Total Pages : 395 pages
Book Rating : 4.1/5 (7 download)

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Book Synopsis Cellular Biophysics and Modeling by : Greg Conradi Smith

Download or read book Cellular Biophysics and Modeling written by Greg Conradi Smith and published by Cambridge University Press. This book was released on 2019-03-14 with total page 395 pages. Available in PDF, EPUB and Kindle. Book excerpt: What every neuroscientist should know about the mathematical modeling of excitable cells, presented at an introductory level.

Computational Genomics with R

Author : Altuna Akalin
Publisher : CRC Press
ISBN 13 : 1498781861
Total Pages : 462 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Computational Genomics with R by : Altuna Akalin

Download or read book Computational Genomics with R written by Altuna Akalin and published by CRC Press. This book was released on 2020-12-16 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.

Computational Structural Biology

Author : Torsten Schwede
Publisher : World Scientific
ISBN 13 : 9812778780
Total Pages : 790 pages
Book Rating : 4.8/5 (127 download)

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Book Synopsis Computational Structural Biology by : Torsten Schwede

Download or read book Computational Structural Biology written by Torsten Schwede and published by World Scientific. This book was released on 2008 with total page 790 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a comprehensive introduction to Landau-Lifshitz equations and Landau-Lifshitz-Maxwell equations, beginning with the work by Yulin Zhou and Boling Guo in the early 1980s and including most of the work done by this Chinese group led by Zhou and Guo since. The book focuses on aspects such as the existence of weak solutions in multi dimensions, existence and uniqueness of smooth solutions in one dimension, relations with harmonic map heat flows, partial regularity and long time behaviors. The book is a valuable reference book for those who are interested in partial differential equations, geometric analysis and mathematical physics. It may also be used as an advanced textbook by graduate students in these fields.

Sequence Comparison

Author : Kun-Mao Chao
Publisher : Springer Science & Business Media
ISBN 13 : 184800320X
Total Pages : 218 pages
Book Rating : 4.8/5 (48 download)

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Book Synopsis Sequence Comparison by : Kun-Mao Chao

Download or read book Sequence Comparison written by Kun-Mao Chao and published by Springer Science & Business Media. This book was released on 2008-11-27 with total page 218 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biomolecular sequence comparison is the origin of bioinformatics. This book gives a complete in-depth treatment of the study of sequence comparison. A comprehensive introduction is followed by a focus on alignment algorithms and techniques, proceeded by a discussion of the theory. The book examines alignment methods and techniques, features a new issue of sequence comparison - the spaced seed technique, addresses several new flexible strategies for coping with various scoring schemes, and covers the theory on the significance of high-scoring segment pairs between two unalignment sequences. Useful appendices on basic concepts in molecular biology, primer in statistics and software for sequence alignment are included in this reader-friendly text, as well as chapter-ending exercise and research questions A state-of-the-art study of sequence alignment and homology search, this is an ideal reference for advanced students studying bioinformatics and will appeal to biologists who wish to know how to use homology search tools.

Bioinformatics Data Skills

Author : Vince Buffalo
Publisher : "O'Reilly Media, Inc."
ISBN 13 : 1449367518
Total Pages : 538 pages
Book Rating : 4.4/5 (493 download)

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Book Synopsis Bioinformatics Data Skills by : Vince Buffalo

Download or read book Bioinformatics Data Skills written by Vince Buffalo and published by "O'Reilly Media, Inc.". This book was released on 2015-07 with total page 538 pages. Available in PDF, EPUB and Kindle. Book excerpt: Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, youâ??ll learn how to use freely available open source tools to extract meaning from large complex biological data sets. At no other point in human history has our ability to understand lifeâ??s complexities been so dependent on our skills to work with and analyze data. This intermediate-level book teaches the general computational and data skills you need to analyze biological data. If you have experience with a scripting language like Python, youâ??re ready to get started. Go from handling small problems with messy scripts to tackling large problems with clever methods and tools Process bioinformatics data with powerful Unix pipelines and data tools Learn how to use exploratory data analysis techniques in the R language Use efficient methods to work with genomic range data and range operations Work with common genomics data file formats like FASTA, FASTQ, SAM, and BAM Manage your bioinformatics project with the Git version control system Tackle tedious data processing tasks with with Bash scripts and Makefiles

A Primer in Mathematical Models in Biology

Author : Lee A. Segel
Publisher : SIAM
ISBN 13 : 1611972493
Total Pages : 435 pages
Book Rating : 4.6/5 (119 download)

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Book Synopsis A Primer in Mathematical Models in Biology by : Lee A. Segel

Download or read book A Primer in Mathematical Models in Biology written by Lee A. Segel and published by SIAM. This book was released on 2013-05-09 with total page 435 pages. Available in PDF, EPUB and Kindle. Book excerpt: A textbook on mathematical modelling techniques with powerful applications to biology, combining theoretical exposition with exercises and examples.

Algebraic and Combinatorial Computational Biology

Author : Raina Robeva
Publisher : Academic Press
ISBN 13 : 0128140690
Total Pages : 434 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Algebraic and Combinatorial Computational Biology by : Raina Robeva

Download or read book Algebraic and Combinatorial Computational Biology written by Raina Robeva and published by Academic Press. This book was released on 2018-10-08 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt: Algebraic and Combinatorial Computational Biology introduces students and researchers to a panorama of powerful and current methods for mathematical problem-solving in modern computational biology. Presented in a modular format, each topic introduces the biological foundations of the field, covers specialized mathematical theory, and concludes by highlighting connections with ongoing research, particularly open questions. The work addresses problems from gene regulation, neuroscience, phylogenetics, molecular networks, assembly and folding of biomolecular structures, and the use of clustering methods in biology. A number of these chapters are surveys of new topics that have not been previously compiled into one unified source. These topics were selected because they highlight the use of technique from algebra and combinatorics that are becoming mainstream in the life sciences. Integrates a comprehensive selection of tools from computational biology into educational or research programs Emphasizes practical problem-solving through multiple exercises, projects and spinoff computational simulations Contains scalable material for use in undergraduate and graduate-level classes and research projects Introduces the reader to freely-available professional software Supported by illustrative datasets and adaptable computer code

Computational Phylogenetics

Author : Tandy Warnow
Publisher : Cambridge University Press
ISBN 13 : 1107184711
Total Pages : 399 pages
Book Rating : 4.1/5 (71 download)

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Book Synopsis Computational Phylogenetics by : Tandy Warnow

Download or read book Computational Phylogenetics written by Tandy Warnow and published by Cambridge University Press. This book was released on 2017-11-02 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the foundations of phylogeny estimation and technical material enabling researchers to develop improved computational methods.