Building Bioinformatics Solutions 2nd Edition

Author: Conrad Bessant,Darren Oakley,Ian Shadforth

Publisher: Oxford University Press

ISBN: 0199658552

Category: Computers

Page: 368

View: 4649

This book introduces the reader to all the key concepts and technologies needed to begin developing their own bioinformatics tools. The new edition includes more bioinformatics-specific content and a new chapter on good software engineering practices to help people working in teams.

Building Bioinformatics Solutions

Author: Robert Elder

Publisher: N.A

ISBN: 9781975792152


Page: 358

View: 4958

Building Bioinformatics Solutions is suitable for graduate students and researchers in the life sciences who wish to automate analyses or create their own databases and web-based tools. No prior knowledge of software development is assumed. Having worked through the book, the reader should have the necessary core skills to develop computational solutions for their specific research programmes. The book will also help the reader overcome the inertia associated with penetrating this field, and provide them with the confidence and understanding required to go on to develop more advanced bioinformatics skills.

Developing Bioinformatics Computer Skills

Author: Cynthia Gibas,Per Jambeck

Publisher: "O'Reilly Media, Inc."

ISBN: 9781565926646

Category: Computers

Page: 427

View: 8466

Offers a structured approach to biological data and the computer tools needed to analyze it, covering UNIX, databases, computation, Perl, data mining, data visualization, and tailoring software to suit specific research needs.

Problems and Solutions in Biological Sequence Analysis

Author: Mark Borodovsky,Svetlana Ekisheva

Publisher: Cambridge University Press

ISBN: 1139458124

Category: Science

Page: N.A

View: 6193

This book is the first of its kind to provide a large collection of bioinformatics problems with accompanying solutions. Notably, the problem set includes all of the problems offered in Biological Sequence Analysis (BSA), by Durbin et al., widely adopted as a required text for bioinformatics courses at leading universities worldwide. Although many of the problems included in BSA as exercises for its readers have been repeatedly used for homework and tests, no detailed solutions for the problems were available. Bioinformatics instructors had therefore frequently expressed a need for fully worked solutions and a larger set of problems for use on courses. This book provides just that: following the same structure as BSA and significantly extending the set of workable problems, it will facilitate a better understanding of the contents of the chapters in BSA and will help its readers develop problem-solving skills that are vitally important for conducting successful research in the growing field of bioinformatics. All of the material has been class-tested by the authors at Georgia Tech, where the first ever M.Sc. degree program in Bioinformatics was held.

Algorithms in Bioinformatics

A Practical Introduction

Author: Wing-Kin Sung

Publisher: CRC Press

ISBN: 9781420070347

Category: Science

Page: 407

View: 3941

Thoroughly Describes Biological Applications, Computational Problems, and Various Algorithmic Solutions Developed from the author’s own teaching material, Algorithms in Bioinformatics: A Practical Introduction provides an in-depth introduction to the algorithmic techniques applied in bioinformatics. For each topic, the author clearly details the biological motivation and precisely defines the corresponding computational problems. He also includes detailed examples to illustrate each algorithm and end-of-chapter exercises for students to familiarize themselves with the topics. Supplementary material is available at This classroom-tested textbook begins with basic molecular biology concepts. It then describes ways to measure sequence similarity, presents simple applications of the suffix tree, and discusses the problem of searching sequence databases. After introducing methods for aligning multiple biological sequences and genomes, the text explores applications of the phylogenetic tree, methods for comparing phylogenetic trees, the problem of genome rearrangement, and the problem of motif finding. It also covers methods for predicting the secondary structure of RNA and for reconstructing the peptide sequence using mass spectrometry. The final chapter examines the computational problem related to population genetics.

Bioinformatics with R Cookbook

Author: Paurush Praveen Sinha

Publisher: Packt Publishing Ltd

ISBN: 1783283149

Category: Computers

Page: 340

View: 6625

This book is an easy-to-follow, stepwise guide to handle real life Bioinformatics problems. Each recipe comes with a detailed explanation to the solution steps. A systematic approach, coupled with lots of illustrations, tips, and tricks will help you as a reader grasp even the trickiest of concepts without difficulty.This book is ideal for computational biologists and bioinformaticians with basic knowledge of R programming, bioinformatics and statistics. If you want to understand various critical concepts needed to develop your computational models in Bioinformatics, then this book is for you. Basic knowledge of R is expected.

Exploring Bioinformatics

Author: Caroline St. Clair,Jonathan E. Visick

Publisher: Jones & Bartlett Publishers

ISBN: 128402346X

Category: Computers

Page: 360

View: 9199

Thoroughly revised and updated, Exploring Bioinformatics: A Project-Based Approach, Second Edition is intended for an introductory course in bioinformatics at the undergraduate level. Through hands-on projects, students are introduced to current biological problems and then explore and develop bioinformatic solutions to these issues. Each chapter presents a key problem, provides basic biological concepts, introduces computational techniques to address the problem, and guides students through the use of existing web-based tools and software solutions. This progression prepares students to tackle the On-Your-Own Project, where they develop their own software solutions. Topics such as antibiotic resistance, genetic disease, and genome sequencing provide context and relevance to capture student interest.

Essential Bioinformatics

Author: Jin Xiong

Publisher: Cambridge University Press

ISBN: 113945062X

Category: Science

Page: N.A

View: 1099

Essential Bioinformatics is a concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field. Written specifically for a life science audience, the basics of bioinformatics are explained, followed by discussions of the state-of-the-art computational tools available to solve biological research problems. All key areas of bioinformatics are covered including biological databases, sequence alignment, genes and promoter prediction, molecular phylogenetics, structural bioinformatics, genomics and proteomics. The book emphasizes how computational methods work and compares the strengths and weaknesses of different methods. This balanced yet easily accessible text will be invaluable to students who do not have sophisticated computational backgrounds. Technical details of computational algorithms are explained with a minimum use of mathematical formulae; graphical illustrations are used in their place to aid understanding. The effective synthesis of existing literature as well as in-depth and up-to-date coverage of all key topics in bioinformatics make this an ideal textbook for all bioinformatics courses taken by life science students and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.

Mathematica for Bioinformatics

A Wolfram Language Approach to Omics

Author: George Mias

Publisher: Springer

ISBN: 3319723774

Category: Science

Page: 384

View: 2990

This book offers a comprehensive introduction to using Mathematica and the Wolfram Language for Bioinformatics. The chapters build gradually from basic concepts and the introduction of the Wolfram Language and coding paradigms in Mathematica, to detailed worked examples derived from typical research applications using Wolfram Language code. The coding examples range from basic sequence analysis, accessing genomic databases, differential gene expression, and machine learning implementations to time series analysis of longitudinal omics experiments, multi-omics integration and building dynamic interactive bioinformatics tools using the Wolfram Language. The topics address the daily bioinformatics needs of a broad audience: experimental users looking to understand and visualize their data, beginner bioinformaticians acquiring coding expertise in providing biological research solutions, and practicing expert bioinformaticians working on omics who wish to expand their toolset to include the Wolfram Language.

Data Algorithms

Recipes for Scaling Up with Hadoop and Spark

Author: Mahmoud Parsian

Publisher: "O'Reilly Media, Inc."

ISBN: 1491906154

Category: Computers

Page: 778

View: 3789

If you are ready to dive into the MapReduce framework for processing large datasets, this practical book takes you step by step through the algorithms and tools you need to build distributed MapReduce applications with Apache Hadoop or Apache Spark. Each chapter provides a recipe for solving a massive computational problem, such as building a recommendation system. You’ll learn how to implement the appropriate MapReduce solution with code that you can use in your projects. Dr. Mahmoud Parsian covers basic design patterns, optimization techniques, and data mining and machine learning solutions for problems in bioinformatics, genomics, statistics, and social network analysis. This book also includes an overview of MapReduce, Hadoop, and Spark. Topics include: Market basket analysis for a large set of transactions Data mining algorithms (K-means, KNN, and Naive Bayes) Using huge genomic data to sequence DNA and RNA Naive Bayes theorem and Markov chains for data and market prediction Recommendation algorithms and pairwise document similarity Linear regression, Cox regression, and Pearson correlation Allelic frequency and mining DNA Social network analysis (recommendation systems, counting triangles, sentiment analysis)

Protein Bioinformatics

From Sequence to Function

Author: M. Michael Gromiha

Publisher: Academic Press

ISBN: 0123884241

Category: Computers

Page: 339

View: 2617

One of the most pressing tasks in biotechnology today is to unlock the function of each of the thousands of new genes identified every day. Scientists do this by analyzing and interpreting proteins, which are considered the task force of a gene. This single source reference covers all aspects of proteins, explaining fundamentals, synthesizing the latest literature, and demonstrating the most important bioinformatics tools available today for protein analysis, interpretation and prediction. Students and researchers of biotechnology, bioinformatics, proteomics, protein engineering, biophysics, computational biology, molecular modeling, and drug design will find this a ready reference for staying current and productive in this fast evolving interdisciplinary field. Explains all aspects of proteins including sequence and structure analysis, prediction of protein structures, protein folding, protein stability, and protein interactions Presents a cohesive and accessible overview of the field, using illustrations to explain key concepts and detailed exercises for students.

Biological Sequence Analysis

Probabilistic Models of Proteins and Nucleic Acids

Author: Richard Durbin,Sean R. Eddy,Anders Krogh,Graeme Mitchison

Publisher: Cambridge University Press

ISBN: 113945739X

Category: Science

Page: N.A

View: 5436

Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.

The Central Nervous System

Author: Per Brodal

Publisher: Oxford University Press

ISBN: 0190228970

Category: Medical

Page: 640

View: 3024

The Fifth edition finds the text of The Central Nervous System thoroughly updated and revised, better equipping students with essential information in the field of clinical neuroscience. This text, reviewed to reflect new information as well as understanding of student needs for critical thinking, contains the systematic, in-depth coverage of topics of great clinical interest. This text seamlessly integrates data from all fields of neuroscience as well as clinical neurology and psychology. This textbook presents the functional properties of clinically-relevant disorders by incorporating data from molecular biology to clinical neurology. Key Features of the Fifth Edition Include... ? Chapters knit together by numerous cross-references and explanations, helping the reader to connect data. ? Carefully selected full color line drawings of the complexities of the nervous system. ? Extensive use of text-boxes provides in-depth material without disturbing the flow of reading. ? Provides a crucial list of references for further reading. While most neurological textbooks are cobbled together by multiple authors on a variety of topics within the field, Dr. Brodal pulls together a cohesive and comprehensive guide to neuroscience. This book reflects Dr. Brodal's concise and easy-to-read style, encouraging reflection and critical thinking in established facts and scientific conjecture. This is the perfect reference for medical, graduate, and undergraduate students alike.

Perl Programming for Biologists

Author: D. Curtis Jamison

Publisher: John Wiley & Sons

ISBN: 9780471430599

Category: Computers

Page: 191

View: 4229

Working on the assumption that the reader has no formal training in programming, Perl Programming for Biologists demonstrates how Perl is used to solve biological problems. Each chapter opens with a set of learning objectives, provides numerous review questions and self-study exercises, and concludes with a bulleted summary of key points. The author incorporates numerous real-life examples throughout the text. Upon completing the book, readers are able to quickly perform such tasks as correcting recurring errors in spreadsheets, scanning a Fasta sequence for every occurrence of an EcoRI site, adapting other writers' scripts to one's own purposes, and most important, writing reusable and maintainable scripts that spare the rote repetition of code.

Beginning Perl for Bioinformatics

An Introduction to Perl for Biologists

Author: James Tisdall

Publisher: "O'Reilly Media, Inc."

ISBN: 9780596550479

Category: Computers

Page: 386

View: 8372

With its highly developed capacity to detect patterns in data, Perl has become one of the most popular languages for biological data analysis. But if you're a biologist with little or no programming experience, starting out in Perl can be a challenge. Many biologists have a difficult time learning how to apply the language to bioinformatics. The most popular Perl programming books are often too theoretical and too focused on computer science for a non-programming biologist who needs to solve very specific problems.Beginning Perl for Bioinformatics is designed to get you quickly over the Perl language barrier by approaching programming as an important new laboratory skill, revealing Perl programs and techniques that are immediately useful in the lab. Each chapter focuses on solving a particular bioinformatics problem or class of problems, starting with the simplest and increasing in complexity as the book progresses. Each chapter includes programming exercises and teaches bioinformatics by showing and modifying programs that deal with various kinds of practical biological problems. By the end of the book you'll have a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to take on more advanced bioinformatics programming. Some of the later chapters focus in greater detail on specific bioinformatics topics. This book is suitable for use as a classroom textbook, for self-study, and as a reference.The book covers: Programming basics and working with DNA sequences and strings Debugging your code Simulating gene mutations using random number generators Regular expressions and finding motifs in data Arrays, hashes, and relational databases Regular expressions and restriction maps Using Perl to parse PDB records, annotations in GenBank, and BLAST output

Thirty Million Words

Building a Child's Brain

Author: Dana Suskind

Publisher: Penguin

ISBN: 0698194322

Category: Family & Relationships

Page: 320

View: 1597

*Nominated for the Books for a Better Life Award* The founder and director of the Thirty Million Words Initiative, Professor Dana Suskind, explains why the most important—and astoundingly simple—thing you can do for your child’s future success in life is to talk to him or her, reveals the recent science behind this truth, and outlines precisely how parents can best put it into practice. The research is in: Academic achievement begins on the first day of life with the first word said by a cooing mother just after delivery. A study by researchers Betty Hart and Todd Risley in 1995 found that some children heard thirty million fewer words by their fourth birthdays than others. The children who heard more words were better prepared when they entered school. These same kids, when followed into third grade, had bigger vocabularies, were stronger readers, and got higher test scores. This disparity in learning is referred to as the achievement gap. Professor Dana Suskind, MD, learned of this thirty million word gap in the course of her work as a cochlear implant surgeon at University of Chicago Medical School and began a new research program along with her sister-in-law, Beth Suskind, to find the best ways to bridge that gap. The Thirty Million Word Initiative has developed programs for parents to show the kind of parent-child communication that enables optimal neural development and has tested the programs in and around Chicago across demographic groups. They boil down to getting parents to follow the three Ts: Tune in to what your child is doing; Talk more to your child using lots of descriptive words; and Take turns with your child as you engage in conversation. Parents are shown how to make the words they serve up more enriching. For example, instead of telling a child, “Put your shoes on,” one might say instead, “It is time to go out. What do we have to do?” The lab's new five-year longitudinal research program has just received funding so they can further corroborate their results. The neuroscience of brain plasticity is some of the most valuable and revolutionary medical science being done today. It enables us to think and do better. It is making a difference in the lives of both the old and young. If you care for children, this landmark book is essential reading. From the Hardcover edition.

Introduction to Mathematical Methods in Bioinformatics

Author: Alexander Isaev

Publisher: Springer Science & Business Media

ISBN: 9783540219736

Category: Science

Page: 294

View: 2527

This book looks at the mathematical foundations of the models currently in use. All existing books on bioinformatics are software-orientated and they concentrate on computer implementations of mathematical models of biology. This book is unique in the sense that it looks at the mathematical foundations of the models, which are crucial for correct interpretation of the outputs of the models.

Building Web Services with Microsoft Azure

Author: Alex Belotserkovskiy,Stephen Kaufman,Nikhil Sachdeva

Publisher: Packt Publishing Ltd

ISBN: 1784395692

Category: Computers

Page: 322

View: 8364

If you are a .NET developer who wants to develop end-to-end RESTful applications in the cloud, then this book is for you. A working knowledge of C# will help you get the most out of this book.

Compulsive Hoarding and Acquiring

Author: Gail Steketee,Randy O. Frost

Publisher: Oxford University Press

ISBN: 0198041071

Category: Psychology

Page: 240

View: 7579

The problem of compulsive hoarding and acquiring is more widespread than commonly believed. It often goes undiagnosed, either because sufferers are ashamed of their compulsions or because they dont believe it is a problem that merits professional attention. As much as two percent of the U.S. population suffers secretly from this condition. However, compulsive hoarding can be an emotionally exhausting, uncontrollable, and sometimes dangerous problem. Written by the developers of this groundbreaking treatment, this manual is the first to present an empirically supported and effective CBT program for treating compulsive hoarding and acquiring. This guide gives clinicians the information to understand hoarding and proven tools to help clients overcome their compulsive behaviors. It teaches individuals how to recognize errors in thinking and uses both imagined and real exposures to teach them the skills they need to manage their problem. Home visits by the clinician are a part of the treatment, as well as consultations with other professionals who might assist if necessary. Homework exercises include behavioral experiments to test personal beliefs about possessions, developing an organization plan and filing system, and sorting and organizing items room-by-room. Designed to be used in conjunction with the corresponding workbook, this therapist guide provides numerous assessment and intervention forms to help clients use the methods described in this program. Complete with case examples and strategies for dealing with problems, this user-friendly guide is a dependable resource that no clinician can do without. TreatmentsThatWorkTM represents the gold standard of behavioral healthcare interventions! · All programs have been rigorously tested in clinical trials and are backed by years of research · A prestigious scientific advisory board, led by series Editor-In-Chief David H. Barlow, reviews and evaluates each intervention to ensure that it meets the highest standard of evidence so you can be confident that you are using the most effective treatment available to date · Our books are reliable and effective and make it easy for you to provide your clients with the best care available · Our corresponding workbooks contain psychoeducational information, forms and worksheets, and homework assignments to keep clients engaged and motivated · A companion website ( offers downloadable clinical tools and helpful resources · Continuing Education (CE) Credits are now available on select titles in collaboration with PsychoEducational Resources, Inc. (PER)

A Handbook of Statistical Analyses using R, Third Edition

Author: Torsten Hothorn,Brian S. Everitt

Publisher: CRC Press

ISBN: 1482204584

Category: Mathematics

Page: 456

View: 9581

Like the best-selling first two editions, A Handbook of Statistical Analyses using R, Third Edition provides an up-to-date guide to data analysis using the R system for statistical computing. The book explains how to conduct a range of statistical analyses, from simple inference to recursive partitioning to cluster analysis. New to the Third Edition Three new chapters on quantile regression, missing values, and Bayesian inference Extra material in the logistic regression chapter that describes a regression model for ordered categorical response variables Additional exercises More detailed explanations of R code New section in each chapter summarizing the results of the analyses Updated version of the HSAUR package (HSAUR3), which includes some slides that can be used in introductory statistics courses Whether you’re a data analyst, scientist, or student, this handbook shows you how to easily use R to effectively evaluate your data. With numerous real-world examples, it emphasizes the practical application and interpretation of results.