Bioinformatics Database Systems

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Bioinformatics Database Systems

Kevin Byron,Katherine G. Herbert,Jason T. L. Wang
Bioinformatics Database Systems Book PDF

Author : Kevin Byron,Katherine G. Herbert,Jason T. L. Wang
Publisher : CRC Press
Page : 246 pages
File Size : 42,8 Mb
Release : 2016-12-19
Category : Computers
ISBN : 9781315388083

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Bioinformatics Database Systems by Kevin Byron,Katherine G. Herbert,Jason T. L. Wang Pdf

Modern biological databases comprise not only data, but also sophisticated query facilities and bioinformatics data analysis tools. This book provides an exploration through the world of Bioinformatics Database Systems. The book summarizes the popular and innovative bioinformatics repositories currently available, including popular primary genetic and protein sequence databases, phylogenetic databases, structure and pathway databases, microarray databases and boutique databases. It also explores the data quality and information integration issues currently involved with managing bioinformatics databases, including data quality issues that have been observed, and efforts in the data cleaning field. Biological data integration issues are also covered in-depth, and the book demonstrates how data integration can create new repositories to address the needs of the biological communities. It also presents typical data integration architectures employed in current bioinformatics databases. The latter part of the book covers biological data mining and biological data processing approaches using cloud-based technologies. General data mining approaches are discussed, as well as specific data mining methodologies that have been successfully deployed in biological data mining applications. Two biological data mining case studies are also included to illustrate how data, query, and analysis methods are integrated into user-friendly systems. Aimed at researchers and developers of bioinformatics database systems, the book is also useful as a supplementary textbook for a one-semester upper-level undergraduate course, or an introductory graduate bioinformatics course. About the Authors Kevin Byron is a PhD candidate in the Department of Computer Science at the New Jersey Institute of Technology. Katherine G. Herbert is Associate Professor of Computer Science at Montclair State University. Jason T.L. Wang is Professor of Bioinformatics and Computer Science at the New Jersey Institute of Technology.

Bioinformatics

Stanley I. Letovsky
Bioinformatics Book PDF

Author : Stanley I. Letovsky
Publisher : Springer
Page : 304 pages
File Size : 43,6 Mb
Release : 2013-04-10
Category : Science
ISBN : 147578404X

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Bioinformatics by Stanley I. Letovsky Pdf

Bioinformatics brings computational methods to the analysis and processing of genomic data. Bioinformatics: Databases and Systems focuses on the issues of system building and data curation that dominate the day-to-day concerns of bioinformatics practitioners. Included are chapters by many of today's leading bioinformatics practitioners, describing most of the current paradigms of system building and curation, including both their strengths and weaknesses. Biological topics covered include sequence databases, metabolic pathways, phenotypes, variety collections, gene expression atlases and neuroinformatics. Species range from bacteria to mammals to plants. Software systems and technologies covered include OPM, CORBA, SRS, KLEISLI, ACEDB, Web-based integration and laboratory workflow. Bioinformatics: Databases and Systems provides a valuable introduction for newcomers to the field, and a useful reference for veterans.

Bioinformatics Database Systems

Kevin Byron,Katherine G. Herbert,Jason T. L. Wang
Bioinformatics Database Systems Book PDF

Author : Kevin Byron,Katherine G. Herbert,Jason T. L. Wang
Publisher : CRC Press
Page : 290 pages
File Size : 54,7 Mb
Release : 2016-12-19
Category : Computers
ISBN : 9781315388090

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Bioinformatics Database Systems by Kevin Byron,Katherine G. Herbert,Jason T. L. Wang Pdf

Modern biological databases comprise not only data, but also sophisticated query facilities and bioinformatics data analysis tools. This book provides an exploration through the world of Bioinformatics Database Systems. The book summarizes the popular and innovative bioinformatics repositories currently available, including popular primary genetic and protein sequence databases, phylogenetic databases, structure and pathway databases, microarray databases and boutique databases. It also explores the data quality and information integration issues currently involved with managing bioinformatics databases, including data quality issues that have been observed, and efforts in the data cleaning field. Biological data integration issues are also covered in-depth, and the book demonstrates how data integration can create new repositories to address the needs of the biological communities. It also presents typical data integration architectures employed in current bioinformatics databases. The latter part of the book covers biological data mining and biological data processing approaches using cloud-based technologies. General data mining approaches are discussed, as well as specific data mining methodologies that have been successfully deployed in biological data mining applications. Two biological data mining case studies are also included to illustrate how data, query, and analysis methods are integrated into user-friendly systems. Aimed at researchers and developers of bioinformatics database systems, the book is also useful as a supplementary textbook for a one-semester upper-level undergraduate course, or an introductory graduate bioinformatics course.

Bioinformatics

David Edwards,Jason Stajich,David Hansen
Bioinformatics Book PDF

Author : David Edwards,Jason Stajich,David Hansen
Publisher : Springer Science & Business Media
Page : 450 pages
File Size : 45,9 Mb
Release : 2009-09-03
Category : Science
ISBN : 9780387927381

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Bioinformatics by David Edwards,Jason Stajich,David Hansen Pdf

Bioinformatics is a relatively new field of research. It evolved from the requirement to process, characterize, and apply the information being produced by DNA sequencing technology. The production of DNA sequence data continues to grow exponentially. At the same time, improved bioinformatics such as faster DNA sequence search methods have been combined with increasingly powerful computer systems to process this information. Methods are being developed for the ever more detailed quantification of gene expression, providing an insight into the function of the newly discovered genes, while molecular genetic tools provide a link between these genes and heritable traits. Genetic tests are now available to determine the likelihood of suffering specific ailments and can predict how plant cultivars may respond to the environment. The steps in the translation of the genetic blueprint to the observed phenotype is being increasingly understood through proteome, metabolome and phenome analysis, all underpinned by advances in bioinformatics. Bioinformatics is becoming increasingly central to the study of biology, and a day at a computer can often save a year or more in the laboratory. The volume is intended for graduate-level biology students as well as researchers who wish to gain a better understanding of applied bioinformatics and who wish to use bioinformatics technologies to assist in their research. The volume would also be of value to bioinformatics developers, particularly those from a computing background, who would like to understand the application of computational tools for biological research. Each chapter would include a comprehensive introduction giving an overview of the fundamentals, aimed at introducing graduate students and researchers from diverse backgrounds to the field and bring them up-to-date on the current state of knowledge. To accommodate the broad range of topics in applied bioinformatics, chapters have been grouped into themes: gene and genome analysis, molecular genetic analysis, gene expression analysis, protein and proteome analysis, metabolome analysis, phenome data analysis, literature mining and bioinformatics tool development. Each chapter and theme provides an introduction to the biology behind the data describes the requirements for data processing and details some of the methods applied to the data to enhance biological understanding.

Bioinformatics

Zoé Lacroix,Terence Critchlow
Bioinformatics Book PDF

Author : Zoé Lacroix,Terence Critchlow
Publisher : Academic Press
Page : 466 pages
File Size : 45,9 Mb
Release : 2003-07-18
Category : Computers
ISBN : 9781558608290

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Bioinformatics by Zoé Lacroix,Terence Critchlow Pdf

The heart of the book lies in the collaboration efforts of eight distinct bioinformatics teams that describe their own unique approaches to data integration and interoperability. Each system receives its own chapter where the lead contributors provide precious insight into the specific problems being addressed by the system, why the particular architecture was chosen, and details on the system's strengths and weaknesses. In closing, the editors provide important criteria for evaluating these systems that bioinformatics professionals will find valuable. * Provides a clear overview of the state-of-the-art in data integration and interoperability in genomics, highlighting a variety of systems and giving insight into the strengths and weaknesses of their different approaches.-

Basic Bioinformatics

S. Gladis Helen Hepsyba
Basic Bioinformatics Book PDF

Author : S. Gladis Helen Hepsyba
Publisher : Mjp Publisher
Page : 248 pages
File Size : 49,6 Mb
Release : 2021-07
Category : Science
ISBN : 8180940705

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Basic Bioinformatics by S. Gladis Helen Hepsyba Pdf

Bioinformatics entails the creation and advancement of databases, algorithms, computational and statistical techniques and theory to solve problems arising from the analysis of biological data. This book is an introductory text that links issues in biology to computer science to offer a clear picture of the principles driving bioinformatics. Database concepts and biological database management systems and designing a biological database have been clearly elucidated. Detailed information on sequence analysis has also been provided. The applications of bioinformatics also have been explained from a genomics and proteomics perspective.

Sequence Data Mining

Guozhu Dong,Jian Pei
Sequence Data Mining Book PDF

Author : Guozhu Dong,Jian Pei
Publisher : Springer Science & Business Media
Page : 150 pages
File Size : 46,5 Mb
Release : 2007-10-31
Category : Computers
ISBN : 9780387699370

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Sequence Data Mining by Guozhu Dong,Jian Pei Pdf

Understanding sequence data, and the ability to utilize this hidden knowledge, will create a significant impact on many aspects of our society. Examples of sequence data include DNA, protein, customer purchase history, web surfing history, and more. This book provides thorough coverage of the existing results on sequence data mining as well as pattern types and associated pattern mining methods. It offers balanced coverage on data mining and sequence data analysis, allowing readers to access the state-of-the-art results in one place.

Bioinformatics and Systems Biology

Frederick Marcus
Bioinformatics and Systems Biology Book PDF

Author : Frederick Marcus
Publisher : Springer Science & Business Media
Page : 296 pages
File Size : 49,5 Mb
Release : 2008-07-22
Category : Science
ISBN : 9783540783534

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Bioinformatics and Systems Biology by Frederick Marcus Pdf

Collaborative research in bioinformatics and systems biology is a key element of modern biology and health research. This book highlights and provides access to many of the methods, environments, results and resources involved, including integral laboratory data generation and experimentation and clinical activities. Collaborative projects embody a research paradigm that connects many of the top scientists, institutions, their resources and research worldwide, resulting in first-class contributions to bioinformatics and systems biology. Central themes include describing processes and results in collaborative research projects using computational biology and providing a guide for researchers to access them. The book is also a practical guide on how science is managed. It shows how collaborative researchers are putting results together in a way accessible to the entire biomedical community.

Bioinformatics Data Skills

Vince Buffalo
Bioinformatics Data Skills Book PDF

Author : Vince Buffalo
Publisher : "O'Reilly Media, Inc."
Page : 538 pages
File Size : 55,7 Mb
Release : 2015-07
Category : Computers
ISBN : 9781449367510

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Bioinformatics Data Skills by Vince Buffalo Pdf

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

Bioinformatics

M. H. Fulekar
Bioinformatics Book PDF

Author : M. H. Fulekar
Publisher : Springer Science & Business Media
Page : 254 pages
File Size : 48,5 Mb
Release : 2009-03-24
Category : Science
ISBN : 9781402088803

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Bioinformatics by M. H. Fulekar Pdf

Bioinformatics, computational biology, is a relatively new field that applies computer science and information technology to biology. In recent years, the discipline of bioinformatics has allowed biologists to make full use of the advances in Computer sciences and Computational statistics for advancing the biological data. Researchers in life sciences generate, collect and need to analyze an increasing number of different types of scientific data, DNA, RNA and protein sequences, in-situ and microarray gene expression including 3D protein structures and biological pathways. This book is aiming to provide information on bioinformatics at various levels. The chapters included in this book cover introductory to advanced aspects, including applications of various documented research work and specific case studies related to bioinformatics. This book will be of immense value to readers of different backgrounds such as engineers, scientists, consultants and policy makers for industry, government, academics and social and private organisations.

Bioinformatics Biocomputing and Perl

Michael Moorhouse,Paul Barry
Bioinformatics Biocomputing and Perl Book PDF

Author : Michael Moorhouse,Paul Barry
Publisher : John Wiley & Sons
Page : 506 pages
File Size : 48,7 Mb
Release : 2005-09-27
Category : Medical
ISBN : 9780470026458

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Bioinformatics Biocomputing and Perl by Michael Moorhouse,Paul Barry Pdf

Bioinformatics, Biocomputing and Perl presents a modern introduction to bioinformatics computing skills and practice. Structuring its presentation around four main areas of study, this book covers the skills vital to the day-to-day activities of today’s bioinformatician. Each chapter contains a series of maxims designed to highlight key points and there are exercises to supplement and cement the introduced material. Working with Perl presents an extended tutorial introduction to programming through Perl, the premier programming technology of the bioinformatics community. Even though no previous programming experience is assumed, completing the tutorial equips the reader with the ability to produce powerful custom programs with ease. Working with Data applies the programming skills acquired to processing a variety of bioinformatics data. In addition to advice on working with important data stores such as the Protein DataBank, SWISS-PROT, EMBL and the GenBank, considerable discussion is devoted to using bioinformatics data to populate relational database systems. The popular MySQL database is used in all examples. Working with the Web presents a discussion of the Web-based technologies that allow the bioinformatics researcher to publish both data and applications on the Internet. Working with Applications shifts gear from creating custom programs to using them. The tools described include Clustal-W, EMBOSS, STRIDE, BLAST and Xmgrace. An introduction to the important Bioperl Project concludes this chapter and rounds off the book.

Bioinformatics for Systems Biology

Stephen Krawetz
Bioinformatics for Systems Biology Book PDF

Author : Stephen Krawetz
Publisher : Springer Science & Business Media
Page : 639 pages
File Size : 41,6 Mb
Release : 2008-12-11
Category : Science
ISBN : 9781597454407

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Bioinformatics for Systems Biology by Stephen Krawetz Pdf

Bioinformatics for Systems Biology bridges and unifies many disciplines. It presents the life scientist, computational biologist, and mathematician with a common framework. Only by linking the groups together may the true life sciences revolution move forward.

Database Systems for Advanced Applications '97

Rodney Topor,Katsumi Tanaka
Database Systems for Advanced Applications 97 Book PDF

Author : Rodney Topor,Katsumi Tanaka
Publisher : World Scientific
Page : 567 pages
File Size : 50,9 Mb
Release : 1997
Category : Computers
ISBN : 9789810231071

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Database Systems for Advanced Applications '97 by Rodney Topor,Katsumi Tanaka Pdf

This volume contains the proceedings of the Fifth International Conference on Database Systems for Advanced Applications (DASFAA '97). DASFAA '97 focused on advanced database technologies and their applications. The 55 papers in this volume cover a wide range of areas in the field of database systems and applications ? including the rapidly emerging areas of the Internet, multimedia, and document database systems ? and should be of great interest to all database system researchers and developers, and practitioners.

Bioinformatics

Zoé Lacroix,Terence Critchlow
Bioinformatics Book PDF

Author : Zoé Lacroix,Terence Critchlow
Publisher : Elsevier
Page : 441 pages
File Size : 46,5 Mb
Release : 2003-09-08
Category : Computers
ISBN : 9780080527987

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Bioinformatics by Zoé Lacroix,Terence Critchlow Pdf

Life science data integration and interoperability is one of the most challenging problems facing bioinformatics today. In the current age of the life sciences, investigators have to interpret many types of information from a variety of sources: lab instruments, public databases, gene expression profiles, raw sequence traces, single nucleotide polymorphisms, chemical screening data, proteomic data, putative metabolic pathway models, and many others. Unfortunately, scientists are not currently able to easily identify and access this information because of the variety of semantics, interfaces, and data formats used by the underlying data sources. Bioinformatics: Managing Scientific Data tackles this challenge head-on by discussing the current approaches and variety of systems available to help bioinformaticians with this increasingly complex issue. The heart of the book lies in the collaboration efforts of eight distinct bioinformatics teams that describe their own unique approaches to data integration and interoperability. Each system receives its own chapter where the lead contributors provide precious insight into the specific problems being addressed by the system, why the particular architecture was chosen, and details on the system's strengths and weaknesses. In closing, the editors provide important criteria for evaluating these systems that bioinformatics professionals will find valuable. * Provides a clear overview of the state-of-the-art in data integration and interoperability in genomics, highlighting a variety of systems and giving insight into the strengths and weaknesses of their different approaches. * Discusses shared vocabulary, design issues, complexity of use cases, and the difficulties of transferring existing data management approaches to bioinformatics systems, which serves to connect computer and life scientists. * Written by the primary contributors of eight reputable bioinformatics systems in academia and industry including: BioKris, TAMBIS, K2, GeneExpress, P/FDM, MBM, SDSC, SRS, and DiscoveryLink.

Bioinformatics

Hamid D. Ismail
Bioinformatics Book PDF

Author : Hamid D. Ismail
Publisher : CRC Press
Page : 466 pages
File Size : 54,7 Mb
Release : 2022-03-23
Category : Science
ISBN : 9781000519075

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Bioinformatics by Hamid D. Ismail Pdf

Bioinformatics: A Practical Guide to NCBI Databases and Sequence Alignments provides the basics of bioinformatics and in-depth coverage of NCBI databases, sequence alignment, and NCBI Sequence Local Alignment Search Tool (BLAST). As bioinformatics has become essential for life sciences, the book has been written specifically to address the need of a large audience including undergraduates, graduates, researchers, healthcare professionals, and bioinformatics professors who need to use the NCBI databases, retrieve data from them, and use BLAST to find evolutionarily related sequences, sequence annotation, construction of phylogenetic tree, and the conservative domain of a protein, to name just a few. Technical details of alignment algorithms are explained with a minimum use of mathematical formulas and with graphical illustrations. Key Features Provides readers with the most-used bioinformatics knowledge of bioinformatics databases and alignments including both theory and application via illustrations and worked examples. Discusses the use of Windows Command Prompt, Linux shell, R, and Python for both Entrez databases and BLAST. The companion website contains tutorials, R and Python codes, instructor materials including slides, exercises, and problems for students. This is the ideal textbook for bioinformatics courses taken by students of life sciences and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.