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Author: Andreas Gogol-Döring
Publisher: CRC Press
ISBN: 1420076248
Category : Computers
Languages : en
Pages : 330
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Book Description
An Easy-to-Use Research Tool for Algorithm Testing and DevelopmentBefore the SeqAn project, there was clearly a lack of available implementations in sequence analysis, even for standard tasks. Implementations of needed algorithmic components were either unavailable or hard to access in third-party monolithic software products. Addressing these conc
Author: Andreas Gogol-Döring
Publisher: CRC Press
ISBN: 1420076248
Category : Computers
Languages : en
Pages : 330
Get Book
Book Description
An Easy-to-Use Research Tool for Algorithm Testing and DevelopmentBefore the SeqAn project, there was clearly a lack of available implementations in sequence analysis, even for standard tasks. Implementations of needed algorithmic components were either unavailable or hard to access in third-party monolithic software products. Addressing these conc
Author: Hannes Hauswedell
Publisher: Springer Nature
ISBN: 3030909905
Category : Computers
Languages : en
Pages : 350
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Book Description
This is a book about software engineering, bioinformatics, the C++ programming language and the SeqAn library. In the broadest sense, it will help the reader create better, faster and more reliable software by deepening their understanding of available tools, language features, techniques and design patterns. Every developer who previously worked with C++ will enjoy the in-depth chapter on important changes in the language from C++11 up to and including C++20. In contrast to many resources on Modern C++ that present new features only in small isolated examples, this book represents a more holistic approach: readers will understand the relevance of new features and how they interact in the context of a large software project and not just within a "toy example". Previous experience in creating software with C++ is highly recommended to fully appreciate these aspects. SeqAn3 is a new, re-designed software library. The conception and implementation process is detailed in this book, including a critical reflection on the previous versions of the library. This is particularly helpful to readers who are about to create a large software project themselves, or who are planning a major overhaul of an existing library or framework. While the focus of the book is clearly on software development and design, it also touches on various organisational and administrative aspects like licensing, dependency management and quality control.
Author: Richard Durbin
Publisher: Cambridge University Press
ISBN: 113945739X
Category : Science
Languages : en
Pages : 372
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Book Description
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.
Author: Emmanuel Barillot
Publisher: CRC Press
ISBN: 1439831459
Category : Computers
Languages : en
Pages : 461
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Book Description
The future of cancer research and the development of new therapeutic strategies rely on our ability to convert biological and clinical questions into mathematical models-integrating our knowledge of tumour progression mechanisms with the tsunami of information brought by high-throughput technologies such as microarrays and next-generation sequencin
Author: Andreas Kremling
Publisher: CRC Press
ISBN: 1466567899
Category : Mathematics
Languages : en
Pages : 382
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Book Description
Drawing on the latest research in the field, Systems Biology: Mathematical Modeling and Model Analysis presents many methods for modeling and analyzing biological systems, in particular cellular systems. It shows how to use predictive mathematical models to acquire and analyze knowledge about cellular systems. It also explores how the models are systematically applied in biotechnology. The first part of the book introduces biological basics, such as metabolism, signaling, gene expression, and control as well as mathematical modeling fundamentals, including deterministic models and thermodynamics. The text also discusses linear regression methods, explains the differences between linear and nonlinear regression, and illustrates how to determine input variables to improve estimation accuracy during experimental design. The second part covers intracellular processes, including enzymatic reactions, polymerization processes, and signal transduction. The author highlights the process–function–behavior sequence in cells and shows how modeling and analysis of signal transduction units play a mediating role between process and function. The third part presents theoretical methods that address the dynamics of subsystems and the behavior near a steady state. It covers techniques for determining different time scales, sensitivity analysis, structural kinetic modeling, and theoretical control engineering aspects, including a method for robust control. It also explores frequent patterns (motifs) in biochemical networks, such as the feed-forward loop in the transcriptional network of E. coli. Moving on to models that describe a large number of individual reactions, the last part looks at how these cellular models are used in biotechnology. The book also explains how graphs can illustrate the link between two components in large networks with several interactions.
Author: Alpan Raval
Publisher: CRC Press
ISBN: 1420010360
Category : Computers
Languages : en
Pages : 329
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Book Description
The new research area of genomics-inspired network biology lacks an introductory book that enables both physical/computational scientists and biologists to obtain a general yet sufficiently rigorous perspective of current thinking. Filling this gap, Introduction to Biological Networks provides a thorough introduction to genomics-inspired network bi
Author: Arnaud Chauvière
Publisher: CRC Press
ISBN: 1420094556
Category : Mathematics
Languages : en
Pages : 484
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Book Description
Ubiquitous and fundamental in cell mechanics, multiscale problems can arise in the growth of tumors, embryogenesis, tissue engineering, and more. Cell Mechanics: From Single Scale-Based Models to Multiscale Modeling brings together new insight and research on mechanical, mathematical, physical, and biological approaches for simulating the behavior
Author: Ken Nguyen
Publisher: John Wiley & Sons
ISBN: 1119272459
Category : Computers
Languages : en
Pages : 256
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Book Description
Covers the fundamentals and techniques of multiple biological sequence alignment and analysis, and shows readers how to choose the appropriate sequence analysis tools for their tasks This book describes the traditional and modern approaches in biological sequence alignment and homology search. This book contains 11 chapters, with Chapter 1 providing basic information on biological sequences. Next, Chapter 2 contains fundamentals in pair-wise sequence alignment, while Chapters 3 and 4 examine popular existing quantitative models and practical clustering techniques that have been used in multiple sequence alignment. Chapter 5 describes, characterizes and relates many multiple sequence alignment models. Chapter 6 describes how traditionally phylogenetic trees have been constructed, and available sequence knowledge bases can be used to improve the accuracy of reconstructing phylogeny trees. Chapter 7 covers the latest methods developed to improve the run-time efficiency of multiple sequence alignment. Next, Chapter 8 covers several popular existing multiple sequence alignment server and services, and Chapter 9 examines several multiple sequence alignment techniques that have been developed to handle short sequences (reads) produced by the Next Generation Sequencing technique (NSG). Chapter 10 describes a Bioinformatics application using multiple sequence alignment of short reads or whole genomes as input. Lastly, Chapter 11 provides a review of RNA and protein secondary structure prediction using the evolution information inferred from multiple sequence alignments. • Covers the full spectrum of the field, from alignment algorithms to scoring methods, practical techniques, and alignment tools and their evaluations • Describes theories and developments of scoring functions and scoring matrices •Examines phylogeny estimation and large-scale homology search Multiple Biological Sequence Alignment: Scoring Functions, Algorithms and Applications is a reference for researchers, engineers, graduate and post-graduate students in bioinformatics, and system biology and molecular biologists. Ken Nguyen, PhD, is an associate professor at Clayton State University, GA, USA. He received his PhD, MSc and BSc degrees in computer science all from Georgia State University. His research interests are in databases, parallel and distribute computing and bioinformatics. He was a Molecular Basis of Disease fellow at Georgia State and is the recipient of the highest graduate honor at Georgia State, the William M. Suttles Graduate Fellowship. Xuan Guo, PhD, is a postdoctoral associate at Oak Ridge National Lab, USA. He received his PhD degree in computer science from Georgia State University in 2015. His research interests are in bioinformatics, machine leaning, and cloud computing. He is an editorial assistant of International Journal of Bioinformatics Research and Applications. Yi Pan, PhD, is a Regents' Professor of Computer Science and an Interim Associate Dean and Chair of Biology at Georgia State University. He received his BE and ME in computer engineering from Tsinghua University in China and his PhD in computer science from the University of Pittsburgh. Dr. Pan's research interests include parallel and distributed computing, optical networks, wireless networks and bioinformatics. He has published more than 180 journal papers with about 60 papers published in various IEEE/ACM journals. He is co-editor along with Albert Y. Zomaya of the Wiley Series in Bioinformatics.
Author: Tieng K. Yap
Publisher: Springer Science & Business Media
ISBN: 1461313910
Category : Computers
Languages : en
Pages : 219
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Book Description
High Performance Computational Methods for Biological Sequence Analysis presents biological sequence analysis using an interdisciplinary approach that integrates biological, mathematical and computational concepts. These concepts are presented so that computer scientists and biomedical scientists can obtain the necessary background for developing better algorithms and applying parallel computational methods. This book will enable both groups to develop the depth of knowledge needed to work in this interdisciplinary field. This work focuses on high performance computational approaches that are used to perform computationally intensive biological sequence analysis tasks: pairwise sequence comparison, multiple sequence alignment, and sequence similarity searching in large databases. These computational methods are becoming increasingly important to the molecular biology community allowing researchers to explore the increasingly large amounts of sequence data generated by the Human Genome Project and other related biological projects. The approaches presented by the authors are state-of-the-art and show how to reduce analysis times significantly, sometimes from days to minutes. High Performance Computational Methods for Biological Sequence Analysis is tremendously important to biomedical science students and researchers who are interested in applying sequence analyses to their studies, and to computational science students and researchers who are interested in applying new computational approaches to biological sequence analyses.
Author: Sorin Draghici
Publisher: CRC Press
ISBN: 1439809763
Category : Computers
Languages : en
Pages : 1036
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Book Description
Richly illustrated in color, Statistics and Data Analysis for Microarrays Using R and Bioconductor, Second Edition provides a clear and rigorous description of powerful analysis techniques and algorithms for mining and interpreting biological information. Omitting tedious details, heavy formalisms, and cryptic notations, the text takes a hands-on,
