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Author: Paul Weston Publisher: John Wiley & Sons ISBN: 0470858346 Category : Medical Languages : en Pages : 140
Book Description
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
Author: Paul Weston Publisher: John Wiley & Sons ISBN: 0470858346 Category : Medical Languages : en Pages : 140
Book Description
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
Author: Hannes Hauswedell Publisher: Springer Nature ISBN: 3030909905 Category : Computers Languages : en Pages : 350
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: Lawrence Baker Publisher: ISBN: 9781641160032 Category : Science Languages : en Pages : 238
Book Description
Bioinformatics is a field which uses the principles and techniques of mathematics, computer science, engineering, statistics, etc. to analyse and interpret biological data. It is also used to understand the complex system of proteomics. The topics studied under this area are DNA sequencing, computational evolutionary biology, pan genomics, gene expression analysis, protein localization, structural bioinformatics, biodiversity informatics, etc. This book unfolds the innovative aspects of bioinformatics which will be crucial for the holistic understanding of the subject matter. It studies, analyses and upholds the pillars of this field and its utmost significance in modern times. This textbook will serve as a reference to a broad spectrum of readers.
Author: Elvis C. Foster Publisher: CRC Press ISBN: 100039381X Category : Computers Languages : en Pages : 621
Book Description
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.
Author: Cynthia Gibas Publisher: "O'Reilly Media, Inc." ISBN: 9781565926646 Category : Computers Languages : en Pages : 452
Book Description
This practical, hands-on guide shows how to develop a structured approach to biological data and the tools needed to analyze it. It's aimed at scientists and students learning computational approaches to biological data, as well as experienced biology researchers starting to use computers to handle data.
Author: Raian Ali Publisher: Springer Nature ISBN: 3030966488 Category : Computers Languages : en Pages : 364
Book Description
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.
Author: Ethan Cerami Publisher: Springer Science & Business Media ISBN: 0387274782 Category : Computers Languages : en Pages : 311
Book Description
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.
Author: Shi Kuo Chang Publisher: World Scientific ISBN: 9812389717 Category : Computers Languages : en Pages : 939
Book Description
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."
Author: Conrad Bessant Publisher: OUP Oxford ISBN: 0191643203 Category : Science Languages : en Pages : 352
Book Description
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.
Author: Paul Weston
Author: Paul Weston
Author: Paul Weston (HGMP.)
Author: Hannes Hauswedell
Author: Lawrence Baker
Author: Elvis C. Foster
Author: Cynthia Gibas
Author: Raian Ali
Author: Ethan Cerami
Author: Shi Kuo Chang
Author: Conrad Bessant