Download or read book Sequence Analysis and Modern C written by Hannes Hauswedell and published by Springer Nature. This book was released on 2022-03-07 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book SeqAn3 Sequence Analysis and Modern C written by Hannes Hauswedell and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Biological Sequence Analysis Using the SeqAn C Library written by Andreas Gogol-Döring and published by CRC Press. This book was released on 2009-11-11 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Genome Scale Algorithm Design written by Veli Mäkinen and published by Cambridge University Press. This book was released on 2015-05-07 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Advances in Sequence Analysis Theory Method Applications written by Philippe Blanchard and published by Springer. This book was released on 2014-07-02 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Sequence Analysis Algorithms for Bioinformatics Application written by Mohamed Issa and published by . This book was released on 2014-10-06 with total page 94 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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."
Download or read book Virus Bioinformatics written by Manja Marz and published by MDPI. This book was released on 2020-02-21 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book From Mathematics to Generic Programming written by Alexander A. Stepanov and published by Addison-Wesley Professional. This book was released on 2014-11-13 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Download or read book The Standard ML Basis Library written by Emden R. Gansner and published by Cambridge University Press. This book was released on 2004-04-05 with total page 486 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Python for Bioinformatics written by Sebastian Bassi and published by CRC Press. This book was released on 2017-08-07 with total page 510 pages. Available in PDF, EPUB and Kindle. Book excerpt: In today's data driven biology, programming knowledge is essential in turning ideas into testable hypothesis. Based on the author’s extensive experience, Python for Bioinformatics, Second Edition helps biologists get to grips with the basics of software development. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language. This new edition is updated throughout to Python 3 and is designed not just to help scientists master the basics, but to do more in less time and in a reproducible way. New developments added in this edition include NoSQL databases, the Anaconda Python distribution, graphical libraries like Bokeh, and the use of Github for collaborative development.
Download or read book Bioinformatics Algorithms written by Miguel Rocha and published by Academic Press. This book was released on 2018-06-08 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics Algorithms: Design and Implementation in Python provides a comprehensive book on many of the most important bioinformatics problems, putting forward the best algorithms and showing how to implement them. The book focuses on the use of the Python programming language and its algorithms, which is quickly becoming the most popular language in the bioinformatics field. Readers will find the tools they need to improve their knowledge and skills with regard to algorithm development and implementation, and will also uncover prototypes of bioinformatics applications that demonstrate the main principles underlying real world applications. - Presents an ideal text for bioinformatics students with little to no knowledge of computer programming - Based on over 12 years of pedagogical materials used by the authors in their own classrooms - Features a companion website with downloadable codes and runnable examples (such as using Jupyter Notebooks) and exercises relating to the book
Download or read book Bioinformatics Programming Using Python written by Mitchell L Model and published by "O'Reilly Media, Inc.". This book was released on 2009-12-08 with total page 526 pages. Available in PDF, EPUB and Kindle. Book excerpt: Powerful, flexible, and easy to use, Python is an ideal language for building software tools and applications for life science research and development. This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. In a short time, you'll be using sophisticated techniques and Python modules that are particularly effective for bioinformatics programming. Bioinformatics Programming Using Python is perfect for anyone involved with bioinformatics -- researchers, support staff, students, and software developers interested in writing bioinformatics applications. You'll find it useful whether you already use Python, write code in another language, or have no programming experience at all. It's an excellent self-instruction tool, as well as a handy reference when facing the challenges of real-life programming tasks. Become familiar with Python's fundamentals, including ways to develop simple applications Learn how to use Python modules for pattern matching, structured text processing, online data retrieval, and database access Discover generalized patterns that cover a large proportion of how Python code is used in bioinformatics Learn how to apply the principles and techniques of object-oriented programming Benefit from the "tips and traps" section in each chapter
Download or read book ACS Style Guide written by Anne M. Coghill and published by American Chemical Society. This book was released on 2006 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the time since the second edition of The ACS Style Guide was published, the rapid growth of electronic communication has dramatically changed the scientific, technical, and medical (STM) publication world. This dynamic mode of dissemination is enabling scientists, engineers, and medicalpractitioners all over the world to obtain and transmit information quickly and easily. An essential constant in this changing environment is the requirement that information remain accurate, clear, unambiguous, and ethically sound.This extensive revision of The ACS Style Guide thoroughly examines electronic tools now available to assist STM writers in preparing manuscripts and communicating with publishers. Valuable updates include discussions of markup languages, citation of electronic sources, online submission ofmanuscripts, and preparation of figures, tables, and structures. In keeping current with the changing environment, this edition also contains references to many resources on the internet.With this wealth of new information, The ACS Style Guide's Third Edition continues its long tradition of providing invaluable insight on ethics in scientific communication, the editorial process, copyright, conventions in chemistry, grammar, punctuation, spelling, and writing style for any STMauthor, reviewer, or editor. The Third Edition is the definitive source for all information needed to write, review, submit, and edit scholarly and scientific manuscripts.
Download or read book Networks in Systems Biology written by Fabricio Alves Barbosa da Silva and published by Springer Nature. This book was released on 2020-10-03 with total page 381 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a range of current research topics in biological network modeling, as well as its application in studies on human hosts, pathogens, and diseases. Systems biology is a rapidly expanding field that involves the study of biological systems through the mathematical modeling and analysis of large volumes of biological data. Gathering contributions from renowned experts in the field, some of the topics discussed in depth here include networks in systems biology, the computational modeling of multidrug-resistant bacteria, and systems biology of cancer. Given its scope, the book is intended for researchers, advanced students, and practitioners of systems biology. The chapters are research-oriented, and present some of the latest findings on their respective topics.
Download or read book The Art of the Metaobject Protocol written by Gregor Kiczales and published by MIT Press. This book was released on 1991-07-30 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: The authors introduce this new approach to programming language design, describe its evolution and design principles, and present a formal specification of a metaobject protocol for CLOS. The CLOS metaobject protocol is an elegant, high-performance extension to the CommonLisp Object System. The authors, who developed the metaobject protocol and who were among the group that developed CLOS, introduce this new approach to programming language design, describe its evolution and design principles, and present a formal specification of a metaobject protocol for CLOS. Kiczales, des Rivières, and Bobrow show that the "art of metaobject protocol design" lies in creating a synthetic combination of object-oriented and reflective techniques that can be applied under existing software engineering considerations to yield a new approach to programming language design that meets a broad set of design criteria. One of the major benefits of including the metaobject protocol in programming languages is that it allows users to adjust the language to better suit their needs. Metaobject protocols also disprove the adage that adding more flexibility to a programming language reduces its performance. In presenting the principles of metaobject protocols, the authors work with actual code for a simplified implementation of CLOS and its metaobject protocol, providing an opportunity for the reader to gain hands-on experience with the design process. They also include a number of exercises that address important concerns and open issues. Gregor Kiczales and Jim des Rivières, are Members of the Research Staff, and Daniel Bobrow is a Research Fellow, in the System Sciences Laboratory at Xerox Palo Alto Research Center.
Download or read book Mastering Python for Bioinformatics written by Ken Youens-Clark and published by "O'Reilly Media, Inc.". This book was released on 2021-05-05 with total page 457 pages. Available in PDF, EPUB and Kindle. Book excerpt: Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained--usually by students and researchers who've never learned basic programming skills. This practical guide shows postdoc bioinformatics professionals and students how to exploit the best parts of Python to solve problems in biology while creating documented, tested, reproducible software. Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates not only how to write effective Python code but also how to use tests to write and refactor scientific programs. You'll learn the latest Python features and toolsâ??including linters, formatters, type checkers, and testsâ??to create documented and tested programs. You'll also tackle 14 challenges in Rosalind, a problem-solving platform for learning bioinformatics and programming. Create command-line Python programs to document and validate parameters Write tests to verify refactor programs and confirm they're correct Address bioinformatics ideas using Python data structures and modules such as Biopython Create reproducible shortcuts and workflows using makefiles Parse essential bioinformatics file formats such as FASTA and FASTQ Find patterns of text using regular expressions Use higher-order functions in Python like filter(), map(), and reduce()
