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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: Hannes Hauswedell
Publisher: Springer Nature
ISBN: 3030909905
Category : Computers
Languages : en
Pages : 350
Get Book Here
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: Hannes Hauswedell
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
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: 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: Veli Mäkinen
Publisher: Cambridge University Press
ISBN: 1316342948
Category : Science
Languages : en
Pages : 415
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Book Description
High-throughput sequencing has revolutionised the field of biological sequence analysis. Its application has enabled researchers to address important biological questions, often for the first time. This book provides an integrated presentation of the fundamental algorithms and data structures that power modern sequence analysis workflows. The topics covered range from the foundations of biological sequence analysis (alignments and hidden Markov models), to classical index structures (k-mer indexes, suffix arrays and suffix trees), Burrows–Wheeler indexes, graph algorithms and a number of advanced omics applications. The chapters feature numerous examples, algorithm visualisations, exercises and problems, each chosen to reflect the steps of large-scale sequencing projects, including read alignment, variant calling, haplotyping, fragment assembly, alignment-free genome comparison, transcript prediction and analysis of metagenomic samples. Each biological problem is accompanied by precise formulations, providing graduate students and researchers in bioinformatics and computer science with a powerful toolkit for the emerging applications of high-throughput sequencing.
Author: Philippe Blanchard
Publisher: Springer
ISBN: 3319049690
Category : Social Science
Languages : en
Pages : 308
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Book Description
This book gives a general view of sequence analysis, the statistical study of successions of states or events. It includes innovative contributions on life course studies, transitions into and out of employment, contemporaneous and historical careers, and political trajectories. The approach presented in this book is now central to the life-course perspective and the study of social processes more generally. This volume promotes the dialogue between approaches to sequence analysis that developed separately, within traditions contrasted in space and disciplines. It includes the latest developments in sequential concepts, coding, atypical datasets and time patterns, optimal matching and alternative algorithms, survey optimization, and visualization. Field studies include original sequential material related to parenting in 19th-century Belgium, higher education and work in Finland and Italy, family formation before and after German reunification, French Jews persecuted in occupied France, long-term trends in electoral participation, and regime democratization. Overall the book reassesses the classical uses of sequences and it promotes new ways of collecting, formatting, representing and processing them. The introduction provides basic sequential concepts and tools, as well as a history of the method. Chapters are presented in a way that is both accessible to the beginner and informative to the expert.
Author: Mohamed Issa
Publisher:
ISBN: 9783656747871
Category :
Languages : de
Pages : 94
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Book Description
Master's Thesis from the year 2014 in the subject Computer Science - Bioinformatics, grade: N, language: English, abstract: The data from next generation sequencing technologies has led to an explosion in genome sequence data available in public databases. This data provides unique opportunities to study the molecular mechanisms of gene evolution: how new genes and proteins originate and how they diversify. A major challenge is retracing origin of extant genes or proteins, by searching existing databases for related sequences and identifying evolutionary similarities. Therefore, enhanced and faster search algorithms are being developed, e.g. on accelerators such as GPU, in order to cope with the huge size of today's DNA or protein sequence databases. Gene-Tracer is a tool was developed to localize the common sub-sequences between two ancestors and its offspring. Besides, compute percentages of ancestors' contributions in offspring. Gene-Tracer was developed to find the origin of unknown shuffling/offspring sequence. A database is scanned and the similarity between offspring sequence and each one in the database is computed using pairwise local sequence alignment algorithm. Based on similarity score, 100 sequences that have the highest score is re-aligned with shuffling sequence to determine length of common sub-sequences between them using local alignment algorithm. The two sequences that have longest sub-sequences with shuffling are the nearest origin to offspring. Swiss-port database contains around 400,000 proteins is used in the test. The execution time around hours. So, GPU is to accelerate the tool. Speedup is 84x using single-GPU Tesla C2075 versus Intel(c) Core i3 multiprocessor. Finally, the main contribution of work is developing fast tool that re-trace origins of unknown gene/protein sequences."
Author: Manja Marz
Publisher: MDPI
ISBN: 3039218824
Category : Science
Languages : en
Pages : 330
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Book Description
Virus bioinformatics is evolving and succeeding as an area of research in its own right, representing the interface of virology and computer science. Bioinformatic approaches to investigate viral infections and outbreaks have become central to virology research, and have been successfully used to detect, control, and treat infections of humans and animals. As part of the Third Annual Meeting of the European Virus Bioinformatics Center (EVBC), we have published this Special Issue on Virus Bioinformatics.
Author: Alexander A. Stepanov
Publisher: Addison-Wesley Professional
ISBN: 0133491781
Category : Computers
Languages : en
Pages : 311
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Book Description
In this substantive yet accessible book, pioneering software designer Alexander Stepanov and his colleague Daniel Rose illuminate the principles of generic programming and the mathematical concept of abstraction on which it is based, helping you write code that is both simpler and more powerful. If you’re a reasonably proficient programmer who can think logically, you have all the background you’ll need. Stepanov and Rose introduce the relevant abstract algebra and number theory with exceptional clarity. They carefully explain the problems mathematicians first needed to solve, and then show how these mathematical solutions translate to generic programming and the creation of more effective and elegant code. To demonstrate the crucial role these mathematical principles play in many modern applications, the authors show how to use these results and generalized algorithms to implement a real-world public-key cryptosystem. As you read this book, you’ll master the thought processes necessary for effective programming and learn how to generalize narrowly conceived algorithms to widen their usefulness without losing efficiency. You’ll also gain deep insight into the value of mathematics to programming—insight that will prove invaluable no matter what programming languages and paradigms you use. You will learn about How to generalize a four thousand-year-old algorithm, demonstrating indispensable lessons about clarity and efficiency Ancient paradoxes, beautiful theorems, and the productive tension between continuous and discrete A simple algorithm for finding greatest common divisor (GCD) and modern abstractions that build on it Powerful mathematical approaches to abstraction How abstract algebra provides the idea at the heart of generic programming Axioms, proofs, theories, and models: using mathematical techniques to organize knowledge about your algorithms and data structures Surprising subtleties of simple programming tasks and what you can learn from them How practical implementations can exploit theoretical knowledge
Author: Emden R. Gansner
Publisher: Cambridge University Press
ISBN: 9781139451406
Category : Computers
Languages : en
Pages : 486
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Book Description
The book provides a description of the Standard ML (SML) Basis Library, the standard library for the SML language. For programmers using SML, it provides a complete description of the modules, types and functions composing the library, which is supported by all conforming implementations of the language. The book serves as a programmer's reference, providing manual pages with concise descriptions. In addition, it presents the principles and rationales used in designing the library, and relates these to idioms and examples for using the library. A particular emphasis of the library is to encourage the use of SML in serious system programming. Major features of the library include I/O, a large collection of primitive types, support for internationalization, and a portable operating system interface. This manual will be an indispensable reference for students, professional programmers, and language designers.
