Sequence Analysis and Modern C++
Sequence Analysis and Modern C++

Author: Hannes Hauswedell

Publisher: Springer Nature

Published: 2022-03-07

Total Pages: 350

ISBN-13: 3030909905

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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.

Biological Sequence Analysis
Biological Sequence Analysis

Author: Richard Durbin

Publisher: Cambridge University Press

Published: 1998-04-23

Total Pages: 372

ISBN-13: 113945739X

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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.

Sequence — Evolution — Function
Sequence — Evolution — Function

Author: Eugene V. Koonin

Publisher: Springer Science & Business Media

Published: 2013-06-29

Total Pages: 482

ISBN-13: 1475737831

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Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.

Modern C++ Design
Modern C++ Design

Author: Andrei Alexandrescu

Publisher: Addison-Wesley Professional

Published: 2001

Total Pages: 352

ISBN-13: 9780201704310

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This title documents a convergence of programming techniques - generic programming, template metaprogramming, object-oriented programming and design patterns. It describes the C++ techniques used in generic programming and implements a number of industrial strength components.

Methods in Protein Sequence Analysis · 1986
Methods in Protein Sequence Analysis · 1986

Author: Kenneth A. Walsh

Publisher: Springer Science & Business Media

Published: 1987-06-17

Total Pages: 654

ISBN-13: 1592594808

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Methods in Protein Sequence Analysis -1986 brings together reports of the most recent methodology available to protein chemists for studying the molecular detail of proteins. The papers in this volume constitute the proceedings of the Sixth International Conference on Methods in Protein Sequence Analysis, which was held at the University of Washington in Seattle, Washington on August 17-21, 1986. This series of conferences has taken place during a period when new techniques in protein chemistry and molecular biology have enabled not only exploration of the control of protein function, but also deduction of the genetic origin of proteins, and labo ratory generation of rare protein molecules for therapeu tic and commercial use. The current reports are focused on the means by which experimental questions can be answered rather than on the biological implications in specific systems. The scope of the meeting was quite broad, empha sizing microanalytical techniques and the relative merits of DNA sequencing, mass spectrometry and more tradi tional degradation techniques. A highlight of the meeting was the Qrowing awareness of the role of mass spec trometry In the analysis of proteins. The complementarity of protein sequencing and DNA sequencing techniques was apparent throughout the discussions and several papers dealt with the strategy of obtaining sequence in formation from small amounts of protein in order that ap propriate oligonucleotide probes could be constructed and the encoding nucleic acids se. quenced and manipu lated.

Methods in Protein Sequence Analysis
Methods in Protein Sequence Analysis

Author: K. Imahori

Publisher: Springer Science & Business Media

Published: 2013-06-29

Total Pages: 307

ISBN-13: 1489916032

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The Ninth International Conference on Methods in Protein Sequence Analysis was held for the first time in Asia from September 20 to September 24, 1992 in Otsu (a city near Kyoto), Japan. Approximately 400 delegates attended the meeting. Forty papers were presented orally and 147 poster presentations were discussed. Academic sessions were held from early in the morning until late in the evening. We are confident that the Conference was successful in providing up-to-date information about methods in protein sequence analysis to all participants. Moreover, with the knowledge and understanding of the present standard of various methods of analysis that are being used and will be used, we were able to clarify areas that need to be evaluated, to be improved and be explored further. Major topics in the Conference mostly covered areas in the methodology of protein sequence analysis, such as: micropreparation and microsequencing of proteins, mass spectrometry, post-translational modification, prediction and database analysis, and analysis of protein structures of special interests. The evolution of genetic engineering in molecular biology has greatly accelerated the accumulation of knowledge on the amino acid sequence of novel proteins regardless of whether they are expressed or not expressed in living organisms. In the early stage of accumulation of structural information, the amino acid sequence itself is worthy of notice.

Post-translational Processing
Post-translational Processing

Author: S. J. Higgins

Publisher: OUP Oxford

Published: 1999-05-20

Total Pages: 338

ISBN-13: 0191566039

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Post - Translational Modification: A Practical Approach and its companion volume Protein Expression: A Practical Approach form the final part of the PAS mini-series on protein synthesis and processing. This volume begins with a chapter on protein sequencing followed by a chapter on protein folding and import into organelles. The next three chapters cover the three major forms of covalent modification: phosphorylation, glycosylation, and lipid modification. Proteolytic processing the is the next topic and the final two chapters are concerned with protein turnover in mammalian cells and yeast. This book is a comprehensive volume of the best current methodology and is designed to be used at the bench or away from the bench to gain insight into future experimental approached.

Effective Modern C++
Effective Modern C++

Author: Scott Meyers

Publisher: "O'Reilly Media, Inc."

Published: 2014-11-11

Total Pages: 334

ISBN-13: 1491908424

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Coming to grips with C++11 and C++14 is more than a matter of familiarizing yourself with the features they introduce (e.g., auto type declarations, move semantics, lambda expressions, and concurrency support). The challenge is learning to use those features effectively—so that your software is correct, efficient, maintainable, and portable. That’s where this practical book comes in. It describes how to write truly great software using C++11 and C++14—i.e. using modern C++. Topics include: The pros and cons of braced initialization, noexcept specifications, perfect forwarding, and smart pointer make functions The relationships among std::move, std::forward, rvalue references, and universal references Techniques for writing clear, correct, effective lambda expressions How std::atomic differs from volatile, how each should be used, and how they relate to C++'s concurrency API How best practices in "old" C++ programming (i.e., C++98) require revision for software development in modern C++ Effective Modern C++ follows the proven guideline-based, example-driven format of Scott Meyers' earlier books, but covers entirely new material. "After I learned the C++ basics, I then learned how to use C++ in production code from Meyer's series of Effective C++ books. Effective Modern C++ is the most important how-to book for advice on key guidelines, styles, and idioms to use modern C++ effectively and well. Don't own it yet? Buy this one. Now". -- Herb Sutter, Chair of ISO C++ Standards Committee and C++ Software Architect at Microsoft

Algebraic and Discrete Mathematical Methods for Modern Biology
Algebraic and Discrete Mathematical Methods for Modern Biology

Author: Raina Robeva

Publisher: Academic Press

Published: 2015-05-09

Total Pages: 383

ISBN-13: 0128012714

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Written by experts in both mathematics and biology, Algebraic and Discrete Mathematical Methods for Modern Biology offers a bridge between math and biology, providing a framework for simulating, analyzing, predicting, and modulating the behavior of complex biological systems. Each chapter begins with a question from modern biology, followed by the description of certain mathematical methods and theory appropriate in the search of answers. Every topic provides a fast-track pathway through the problem by presenting the biological foundation, covering the relevant mathematical theory, and highlighting connections between them. Many of the projects and exercises embedded in each chapter utilize specialized software, providing students with much-needed familiarity and experience with computing applications, critical components of the "modern biology" skill set. This book is appropriate for mathematics courses such as finite mathematics, discrete structures, linear algebra, abstract/modern algebra, graph theory, probability, bioinformatics, statistics, biostatistics, and modeling, as well as for biology courses such as genetics, cell and molecular biology, biochemistry, ecology, and evolution. - Examines significant questions in modern biology and their mathematical treatments - Presents important mathematical concepts and tools in the context of essential biology - Features material of interest to students in both mathematics and biology - Presents chapters in modular format so coverage need not follow the Table of Contents - Introduces projects appropriate for undergraduate research - Utilizes freely accessible software for visualization, simulation, and analysis in modern biology - Requires no calculus as a prerequisite - Provides a complete Solutions Manual - Features a companion website with supplementary resources

Discovering Modern C++
Discovering Modern C++

Author: Peter Gottschling

Publisher: Addison-Wesley Professional

Published: 2015-12-23

Total Pages: 1559

ISBN-13: 0134383664

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As scientific and engineering projects grow larger and more complex, it is increasingly likely that those projects will be written in C++. With embedded hardware growing more powerful, much of its software is moving to C++, too. Mastering C++ gives you strong skills for programming at nearly every level, from “close to the hardware” to the highest-level abstractions. In short, C++ is a language that scientific and technical practitioners need to know. Peter Gottschling’s Discovering Modern C++ is an intensive introduction that guides you smoothly to sophisticated approaches based on advanced features. Gottschling introduces key concepts using examples from many technical problem domains, drawing on his extensive experience training professionals and teaching C++ to students of physics, math, and engineering. This book is designed to help you get started rapidly and then master increasingly robust features, from lambdas to expression templates. You’ll also learn how to take advantage of the powerful libraries available to C++ programmers: both the Standard Template Library (STL) and scientific libraries for arithmetic, linear algebra, differential equations, and graphs. Throughout, Gottschling demonstrates how to write clear and expressive software using object orientation, generics, metaprogramming, and procedural techniques. By the time you’re finished, you’ll have mastered all the abstractions you need to write C++ programs with exceptional quality and performance.