Download or read book Bioinformatics Software Engineering written by Paul Weston and published by John Wiley & Sons. This book was released on 2005-09-01 with total page 140 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics Software Engineering: Delivering Effective Applications will be useful to anyone who wants to understand how successful software can be developed in a rapidly changing environment. A handbook, not a textbook, it is not tied to any particular operating system, platform, language, or methodology. Instead it focuses on principles and practices that have been proven in the real world. It is pragmatic, emphasizing the importance of what the author calls Adaptive Programming - doing what works in your situation, and it is concise, covering the whole software development lifecycle in one slim volume. At each stage, it describes common pitfalls, explains how these can be avoided, and suggests simple techniques which make it easier to deliver better solutions. "Well thought-out ... addresses many of the key issues facing developers of bioinformatics software." (Simon Dear, Director, UK Technology and Development, Bioinformatics Engineering and Integration, Genetics Research, GlaxoSmithKline) Here are some examples from the book itself. On software development: “Writing software properly involves talking to people – often lots of people – and plenty of non-coding work on your part. It requires the ability to dream up new solutions to problems so complicated that they are hard to describe.” From description to specification: “Look for verbs – action words, such as ‘does’, ‘is’ and ‘views’. Identify nouns – naming words, like ‘user’, ‘home’ and ‘sequence’. List the adjectives – describing words, for example ‘quick’, ‘simple’ or ‘precise’. The verbs are the functions that must be provided by your application. The nouns define the parameters to those functions, and the adjectives specify the constraint conditions under which your program must operate.” On how to start writing software: “Handle errors. Take in data. Show output. Get going!” On testing: “It may not be physically possible to test every potential combination of situations that could occur as users interact with a program. But one thing that can be done is to test an application at the agreed extremes of its capability: the maximum number of simultaneous users it has to support, the minimum system configuration it must run on, the lowest communication speed it must cope with, and the most complex operations it must perform. If your program can cope with conditions at the edge of its performance envelope, it is less likely to encounter difficulties in dealing with less challenging situations.” On showing early versions of software to users: “It can be hard explaining the software development process to people who are unfamiliar with it. Code that to you is nearly finished is simply not working to them, and seeing their dream in bits on the workbench can be disappointing to customers, especially when they were expecting to be able to take it for a test drive.” On bugs: “If your users find a genuinely reproducible bug in production code, apologize, fix it fast, and then fix the system that allowed it through. And tell your customers what you are doing, and why, so they will be confident that it will not happen again. Everybody makes mistakes. Don’t make the same ones twice.” And one last thought on successful software development: "You have to be a detective, following up clues and examining evidence to discover what has gone wrong and why. And you have to be a politician, underst

Download or read book Bioinformatics Software Engineering written by Paul Weston (HGMP.) and published by . This book was released on 2004 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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 Software Engineering written by Elvis C. Foster and published by CRC Press. This book was released on 2021-07-20 with total page 621 pages. Available in PDF, EPUB and Kindle. Book excerpt: Software Engineering: A Methodical Approach (Second Edition) provides a comprehensive, but concise introduction to software engineering. It adopts a methodical approach to solving software engineering problems, proven over several years of teaching, with outstanding results. The book covers concepts, principles, design, construction, implementation, and management issues of software engineering. Each chapter is organized systematically into brief, reader-friendly sections, with itemization of the important points to be remembered. Diagrams and illustrations also sum up the salient points to enhance learning. Additionally, the book includes the author’s original methodologies that add clarity and creativity to the software engineering experience. New in the Second Edition are chapters on software engineering projects, management support systems, software engineering frameworks and patterns as a significant building block for the design and construction of contemporary software systems, and emerging software engineering frontiers. The text starts with an introduction of software engineering and the role of the software engineer. The following chapters examine in-depth software analysis, design, development, implementation, and management. Covering object-oriented methodologies and the principles of object-oriented information engineering, the book reinforces an object-oriented approach to the early phases of the software development life cycle. It covers various diagramming techniques and emphasizes object classification and object behavior. The text features comprehensive treatments of: Project management aids that are commonly used in software engineering An overview of the software design phase, including a discussion of the software design process, design strategies, architectural design, interface design, database design, and design and development standards User interface design Operations design Design considerations including system catalog, product documentation, user message management, design for real-time software, design for reuse, system security, and the agile effect Human resource management from a software engineering perspective Software economics Software implementation issues that range from operating environments to the marketing of software Software maintenance, legacy systems, and re-engineering This textbook can be used as a one-semester or two-semester course in software engineering, augmented with an appropriate CASE or RAD tool. It emphasizes a practical, methodical approach to software engineering, avoiding an overkill of theoretical calculations where possible. The primary objective is to help students gain a solid grasp of the activities in the software development life cycle to be confident about taking on new software engineering projects.

Download or read book Java for Bioinformatics and Biomedical Applications written by Harshawardhan Bal and published by Springer Science & Business Media. This book was released on 2007-01-16 with total page 353 pages. Available in PDF, EPUB and Kindle. Book excerpt: Medical science and practice have undergone fundamental changes in the last 5 years, as large-scale genome projects have resulted in the sequencing of a number of important microbial, plant and animal genomes. This book aims to combine industry standard software engineering and design principles with genomics, bioinformatics and cancer research. Rather than an exercise in learning a programming platform, the text focuses on useful analytical tools for the scientific community.

Download or read book XML for Bioinformatics written by Ethan Cerami and published by Springer Science & Business Media. This book was released on 2006-06-02 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduction The goal of this book is to introduce XML to a bioinformatics audience. It does so by introducing the fundamentals of XML, Document Type De?nitions (DTDs), XML Namespaces, XML Schema, and XML parsing, and illustrating these concepts with speci?c bioinformatics case studies. The book does not assume any previous knowledge of XML and is geared toward those who want a solid introduction to fundamental XML concepts. The book is divided into nine chapters: Chapter 1: Introduction to XML for Bioinformatics. This chapter provides an introduction to XML and describes the use of XML in biological data exchange. A bird’s-eye view of our ?rst case study, the Distributed Annotation System (DAS), is provided and we examine a sample DAS XML document. The chapter concludes with a discussion of the pros and cons of using XML in bioinformatic applications. Chapter 2: Fundamentals of XML and BSML. This chapter introduces the fundamental concepts of XML and the Bioinformatic Sequence Markup Language (BSML). We explore the origins of XML, de?ne basic rules for XML document structure, and introduce XML Na- spaces. We also explore several sample BSML documents and visualize these documents in the TM Rescentris Genomic Workspace Viewer.

Download or read book Evaluation of Novel Approaches to Software Engineering written by Raian Ali and published by Springer Nature. This book was released on 2022-02-10 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: The present book includes extended and revised versions of a set of selected papers from the 16th International Conference on Evaluation of Novel Approaches to Software Engineering (ENASE 2021), held as an online event from April 26 to 27, 2021. The 15 revised full papers presented were carefully reviewed and selected from 96 submissions. The papers included in this book contribute to the understanding of relevant trends of current research on novel approaches to software engineering for the development and maintenance of systems and applications, specically with relation to: model-driven software engineering, requirements engineering, empirical software engineering, service-oriented software engineering, business process management and engineering, knowledge management and engineering, reverse software engineering, software process improvement, software change and configuration management, software metrics, software patterns and refactoring, application integration, software architecture, cloud computing, and formal methods.

Download or read book Handbook of Software Engineering and Knowledge Engineering written by Shi Kuo Chang and published by World Scientific. This book was released on 2001 with total page 939 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first handbook to cover comprehensively both software engineering and knowledge engineering OCo two important fields that have become interwoven in recent years. Over 60 international experts have contributed to the book. Each chapter has been written in such a way that a practitioner of software engineering and knowledge engineering can easily understand and obtain useful information. Each chapter covers one topic and can be read independently of other chapters, providing both a general survey of the topic and an in-depth exposition of the state of the art. Practitioners will find this handbook useful when looking for solutions to practical problems. Researchers can use it for quick access to the background, current trends and most important references regarding a certain topic. The handbook consists of two volumes. Volume One covers the basic principles and applications of software engineering and knowledge engineering. Volume Two will cover the basic principles and applications of visual and multimedia software engineering, knowledge engineering, data mining for software knowledge, and emerging topics in software engineering and knowledge engineering. Sample Chapter(s). Chapter 1.1: Introduction (97k). Chapter 1.2: Theoretical Language Research (97k). Chapter 1.3: Experimental Science (96k). Chapter 1.4: Evolutionary Versus Revolutionary (108k). Chapter 1.5: Concurrency and Parallelisms (232k). Chapter 1.6: Summary (123k). Contents: Computer Language Advances (D E Cooke et al.); Software Maintenance (G Canfora & A Cimitile); Requirements Engineering (A T Berztiss); Software Engineering Standards: Review and Perspectives (Y-X Wang); A Large Scale Neural Network and Its Applications (D Graupe & H Kordylewski); Software Configuration Management in Software and Hypermedia Engineering: A Survey (L Bendix et al.); The Knowledge Modeling Paradigm in Knowledge Engineering (E Motta); Software Engineering and Knowledge Engineering Issues in Bioinformatics (J T L Wang et al.); Conceptual Modeling in Software Engineering and Knowledge Engineering: Concepts, Techniques and Trends (O Dieste et al.); Rationale Management in Software Engineering (A H Dutoit & B Paech); Exploring Ontologies (Y Kalfoglou), and other papers. Readership: Graduate students, researchers, programmers, managers and academics in software engineering and knowledge engineering."

Download or read book Discovering Genomics Proteomics and Bioinformatics written by A. Malcolm Campbell and published by Benjamin-Cummings Publishing Company. This book was released on 2007 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discovering Genomics is the first genomics text that combines web activities and case studies with a problem-solving approach to teach upper-level undergraduates and first-year graduate students the fundamentals of genomic analysis. More of a workbook than a traditional text, Discovering Genomics, Second Edition allows students to work with real genomic data in solving problems and provides the user with an active learning experience. The companion website at www.aw-bc.com/geneticsplace is regularly updated to keep up with changes to online databases. The Second Edition has been thoroughly revised and updated to incorporate the latest scientific findings on popular topics such as disease-causing organisms and genetic defects. Case study chapters have been placed throughout the book to tie real-life scenarios into the concepts that follow. Two of the book's key pedagogical features, Discovery Questions and Math Minutes, have also been updated and expanded. The interactive companion website has been reprogrammed with JMOL, the latest 3-D software used to view DNA structures.

Download or read book Building Bioinformatics Solutions written by Conrad Bessant and published by OUP Oxford. This book was released on 2014-01-16 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics encompasses a broad and ever-changing range of activities involved with the management and analysis of data from molecular biology experiments. Despite the diversity of activities and applications, the basic methodology and core tools needed to tackle bioinformatics problems is common to many projects. This unique book provides an invaluable introduction to three of the main tools used in the development of bioinformatics software - Perl, R and MySQL - and explains how these can be used together to tackle the complex data-driven challenges that typify modern biology. These industry standard open source tools form the core of many bioinformatics projects, both in academia and industry. The methodologies introduced are platform independent, and all the examples that feature have been tested on Windows, Linux and Mac OS. Building Bioinformatics Solutions is suitable for graduate students and researchers in the life sciences who wish to automate analyses or create their own databases and web-based tools. No prior knowledge of software development is assumed. Having worked through the book, the reader should have the necessary core skills to develop computational solutions for their specific research programmes. The book will also help the reader overcome the inertia associated with penetrating this field, and provide them with the confidence and understanding required to go on to develop more advanced bioinformatics skills.

Download or read book Advances in Machine Learning Applications in Software Engineering written by Zhang, Du and published by IGI Global. This book was released on 2006-10-31 with total page 498 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book provides analysis, characterization and refinement of software engineering data in terms of machine learning methods. It depicts applications of several machine learning approaches in software systems development and deployment, and the use of machine learning methods to establish predictive models for software quality while offering readers suggestions by proposing future work in this emerging research field"--Provided by publisher.

Download or read book Deep Learning in Bioinformatics written by Habib Izadkhah and published by Academic Press. This book was released on 2022-01-08 with total page 382 pages. Available in PDF, EPUB and Kindle. Book excerpt: Deep Learning in Bioinformatics: Techniques and Applications in Practice introduces the topic in an easy-to-understand way, exploring how it can be utilized for addressing important problems in bioinformatics, including drug discovery, de novo molecular design, sequence analysis, protein structure prediction, gene expression regulation, protein classification, biomedical image processing and diagnosis, biomolecule interaction prediction, and in systems biology. The book also presents theoretical and practical successes of deep learning in bioinformatics, pointing out problems and suggesting future research directions. Dr. Izadkhah provides valuable insights and will help researchers use deep learning techniques in their biological and bioinformatics studies. Introduces deep learning in an easy-to-understand way Presents how deep learning can be utilized for addressing some important problems in bioinformatics Presents the state-of-the-art algorithms in deep learning and bioinformatics Introduces deep learning libraries in bioinformatics

Download or read book Encyclopedia of Software Engineering Three Volume Set Print written by Phillip A. Laplante and published by CRC Press. This book was released on 2010-11-22 with total page 1441 pages. Available in PDF, EPUB and Kindle. Book excerpt: Software engineering requires specialized knowledge of a broad spectrum of topics, including the construction of software and the platforms, applications, and environments in which the software operates as well as an understanding of the people who build and use the software. Offering an authoritative perspective, the two volumes of the Encyclopedia of Software Engineering cover the entire multidisciplinary scope of this important field. More than 200 expert contributors and reviewers from industry and academia across 21 countries provide easy-to-read entries that cover software requirements, design, construction, testing, maintenance, configuration management, quality control, and software engineering management tools and methods. Editor Phillip A. Laplante uses the most universally recognized definition of the areas of relevance to software engineering, the Software Engineering Body of Knowledge (SWEBOK®), as a template for organizing the material. Also available in an electronic format, this encyclopedia supplies software engineering students, IT professionals, researchers, managers, and scholars with unrivaled coverage of the topics that encompass this ever-changing field. Also Available Online This Taylor & Francis encyclopedia is also available through online subscription, offering a variety of extra benefits for researchers, students, and librarians, including: Citation tracking and alerts Active reference linking Saved searches and marked lists HTML and PDF format options Contact Taylor and Francis for more information or to inquire about subscription options and print/online combination packages. US: (Tel) 1.888.318.2367; (E-mail) [email protected] International: (Tel) +44 (0) 20 7017 6062; (E-mail) [email protected]

Download or read book Biomedical Engineering Concepts Methodologies Tools and Applications written by Management Association, Information Resources and published by IGI Global. This book was released on 2017-07-13 with total page 1463 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technological tools and computational techniques have enhanced the healthcare industry. These advancements have led to significant progress and novel opportunities for biomedical engineering. Biomedical Engineering: Concepts, Methodologies, Tools, and Applications is an authoritative reference source for emerging scholarly research on trends, techniques, and future directions in the field of biomedical engineering technologies. Highlighting a comprehensive range of topics such as nanotechnology, biomaterials, and robotics, this multi-volume book is ideally designed for medical practitioners, professionals, students, engineers, and researchers interested in the latest developments in biomedical technology.

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 Bioinformatics Data Skills written by Vince Buffalo and published by "O'Reilly Media, Inc.". This book was released on 2015-07 with total page 538 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Structural Bioinformatics Tools for Drug Design written by Jaroslav Koča and published by Springer. This book was released on 2017-01-24 with total page 144 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book describes the individual steps necessary for biomacromolecular fragments analysis, as well as a list of essential software tools. For each step, it also shows corresponding web-based tools in detail and provides practical examples of their use. All tools and databases mentioned in the examples are available free of charge, platform-independent, web-based, user-friendly and do not require a prior IT background to be fully used.