Bioinformatics Software Engineering
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Bioinformatics Software Engineering
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Author : Paul Weston
language : en
Publisher: John Wiley & Sons
Release Date : 2005-09-01
Bioinformatics Software Engineering written by Paul Weston and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-09-01 with Medical categories.
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
Bioinformatics Software Engineering
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Author : Paul Weston (HGMP.)
language : en
Publisher:
Release Date : 2004
Bioinformatics Software Engineering written by Paul Weston (HGMP.) and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with Bioinformatics categories.
Sequence Analysis And Modern C
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Author : Hannes Hauswedell
language : en
Publisher: Springer Nature
Release Date : 2022-03-07
Sequence Analysis And Modern C written by Hannes Hauswedell and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-03-07 with Computers categories.
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.
Bioinformatics Software Engineering
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Author : Paul Weston
language : en
Publisher: Wiley
Release Date : 2004-11-30
Bioinformatics Software Engineering written by Paul Weston and has been published by Wiley this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004-11-30 with Medical categories.
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, understanding what people want, both in public and in private, and how this is likely to affect what you are trying to do. This book cannot teach you how to do all of that, but it can help."
Xml For Bioinformatics
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Author : Ethan Cerami
language : en
Publisher: Springer Science & Business Media
Release Date : 2006-06-02
Xml For Bioinformatics written by Ethan Cerami and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-06-02 with Computers categories.
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.
User Level Workflow Design
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Author : Anna-Lena Lamprecht
language : en
Publisher: Springer
Release Date : 2013-12-09
User Level Workflow Design written by Anna-Lena Lamprecht and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-12-09 with Computers categories.
The continuous trend in computer science to lift programming to higher abstraction levels increases scalability and opens programming to a wider public. In particular, service-oriented programming and the support of semantics-based frameworks make application development accessible to users with almost no programming expertise. This monograph establishes requirement-centric scientific workflow design as an instance of consequent constraint-driven development. Requirements formulated in terms of user-level constraints are automatically transformed into running applications using temporal logic-based synthesis technology. The impact of this approach is illustrated by applying it to four very different bioinformatics scenarios: phylogenetic analysis, the dedicated GeneFisher-P scenario, the FiatFlux-P scenario, and microarray data analyses.
New Trends In Software Methodologies Tools And Techniques
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Author : H. Fujita
language : en
Publisher: IOS Press
Release Date : 2016-08-30
New Trends In Software Methodologies Tools And Techniques written by H. Fujita and has been published by IOS Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-08-30 with Computers categories.
Software has become an essential enabler for science and the economy. Not only does it create new markets and the possibility of a more reliable, flexible and robust society, it also empowers our exploration of the world in ever increasing depth. However software often falls short of our expectations, with current methodologies, tools and techniques remaining insufficiently robust and reliable for constantly changing and evolving needs. This book presents papers from the 15th International Conference on New Trends in Intelligent Software Methodology Tools and Techniques (SoMeT 16), held in Larnaca, Cyprus, in September 2016. The SoMeT conference focuses on exploring the innovations, controversies and challenges facing the software engineering community, bringing together theory and experience to propose and evaluate solutions to software engineering problems with an emphasis on human-centric software methodologies, end-user development techniques, and emotional reasoning, for an optimally harmonized performance between the design tool and the user. The book is divided into six chapters covering the following areas: decision support systems; software methodologies and tools; requirement engineering; software for biomedicine and bioinformatics; software engineering models, and formal techniques for software representation; and intelligent software development and social networking. The book explores new trends and theories which illuminate the direction of developments in the field, and will be of interest to all in the software science community.
Deep Learning In Bioinformatics
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Author : Habib Izadkhah
language : en
Publisher: Academic Press
Release Date : 2022-01-08
Deep Learning In Bioinformatics written by Habib Izadkhah and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-01-08 with Science categories.
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
A Collaborative Framework For Knowledge Acquisition And Management For Bioinformatics Applications
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Author : Keywan Hodaei Esfahani
language : en
Publisher:
Release Date : 2008
A Collaborative Framework For Knowledge Acquisition And Management For Bioinformatics Applications written by Keywan Hodaei Esfahani and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with categories.
Building Bioinformatics Solutions 2nd Edition
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Author : Conrad Bessant
language : en
Publisher: Oxford University Press
Release Date : 2014
Building Bioinformatics Solutions 2nd Edition written by Conrad Bessant and has been published by Oxford University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with Computers categories.
This book introduces the reader to all the key concepts and technologies needed to begin developing their own bioinformatics tools. The new edition includes more bioinformatics-specific content and a new chapter on good software engineering practices to help people working in teams.