Mark D. LeBlanc and Betsey Dexter Dyer
- Published in print:
- 2007
- Published Online:
- April 2010
- ISBN:
- 9780195305890
- eISBN:
- 9780199773862
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195305890.003.02
- Subject:
- Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies
Clear directions for Mac OS X and Windows users alike are provided to get these respective hardware systems set up for programming in Perl. This chapter provides as much encouragement and support as ...
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Clear directions for Mac OS X and Windows users alike are provided to get these respective hardware systems set up for programming in Perl. This chapter provides as much encouragement and support as possible. Getting through the chapter with success will make the activities of the subsequent chapters possible. The instructions here are the sine qua non of the rest of the book because they tell how to get ‘Perl’ up and running. Side boxes include encouragement for forging new research relationships.Less
Clear directions for Mac OS X and Windows users alike are provided to get these respective hardware systems set up for programming in Perl. This chapter provides as much encouragement and support as possible. Getting through the chapter with success will make the activities of the subsequent chapters possible. The instructions here are the sine qua non of the rest of the book because they tell how to get ‘Perl’ up and running. Side boxes include encouragement for forging new research relationships.
Mark D. LeBlanc and Betsey Dexter Dyer
- Published in print:
- 2007
- Published Online:
- April 2010
- ISBN:
- 9780195305890
- eISBN:
- 9780199773862
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195305890.001.0001
- Subject:
- Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies
The book presents a hands-on introductory guide to DNA sequence analysis. This can be depicted as a linear map of As, Cs, Gs, and Ts; however, such a map only hints at the varied contours and ...
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The book presents a hands-on introductory guide to DNA sequence analysis. This can be depicted as a linear map of As, Cs, Gs, and Ts; however, such a map only hints at the varied contours and crevices, twists, kinks, loops, and nodes of the extraordinary double helix. The book uncovers why Perl is the language of choice when identifying patterns in strings of text. It offers a simplified approach to programming that is applicable to biological sequence analysis, especially geared to those who do not have prior programming experience. Concepts include good programming practices, creative approaches to teaching and working with strings and files of sequence data, and sequence related applications of regular expressions, control structures, arrays, and hash tables. A linguistic metaphor is used throughout the text to complement an exceptionally friendly and pedagogically sound introduction to sequence analysis via Perl programming.Less
The book presents a hands-on introductory guide to DNA sequence analysis. This can be depicted as a linear map of As, Cs, Gs, and Ts; however, such a map only hints at the varied contours and crevices, twists, kinks, loops, and nodes of the extraordinary double helix. The book uncovers why Perl is the language of choice when identifying patterns in strings of text. It offers a simplified approach to programming that is applicable to biological sequence analysis, especially geared to those who do not have prior programming experience. Concepts include good programming practices, creative approaches to teaching and working with strings and files of sequence data, and sequence related applications of regular expressions, control structures, arrays, and hash tables. A linguistic metaphor is used throughout the text to complement an exceptionally friendly and pedagogically sound introduction to sequence analysis via Perl programming.
Mark D. LeBlanc and Betsey Dexter Dyer
- Published in print:
- 2007
- Published Online:
- April 2010
- ISBN:
- 9780195305890
- eISBN:
- 9780199773862
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195305890.003.01
- Subject:
- Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies
This chapter justifies the reason for and approach of this book using examples from diverse sources, including reasons for writing programs for analyzing DNA sequences and the use of collecting, ...
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This chapter justifies the reason for and approach of this book using examples from diverse sources, including reasons for writing programs for analyzing DNA sequences and the use of collecting, cataloguing, annotating, and indexing as tools for scientific exploration and discovery. We are experiencing once again an age of exploration and discovery via the old-fashioned activities of collecting and cataloguing, this time not only organisms, but also DNA sequences. Billions of bases of un-described, essentially unexamined sequences are being stockpiled in the databases of the National Center for Biotechnology Information (NCBI), and other major public databases. The sequences are available for anyone to study. Encouragement to learn to write small Perl scripts to manage sequence data is provided with sixteen reasons to write your own code. Side boxes include finding motifs with your word processor and annotating sequences by hand.Less
This chapter justifies the reason for and approach of this book using examples from diverse sources, including reasons for writing programs for analyzing DNA sequences and the use of collecting, cataloguing, annotating, and indexing as tools for scientific exploration and discovery. We are experiencing once again an age of exploration and discovery via the old-fashioned activities of collecting and cataloguing, this time not only organisms, but also DNA sequences. Billions of bases of un-described, essentially unexamined sequences are being stockpiled in the databases of the National Center for Biotechnology Information (NCBI), and other major public databases. The sequences are available for anyone to study. Encouragement to learn to write small Perl scripts to manage sequence data is provided with sixteen reasons to write your own code. Side boxes include finding motifs with your word processor and annotating sequences by hand.
Bruce Zuckerman
- Published in print:
- 1991
- Published Online:
- October 2011
- ISBN:
- 9780195058963
- eISBN:
- 9780199853342
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780195058963.003.0008
- Subject:
- Religion, Buddhism
The interpretations of the story of Bontsye Shvayg by Hilde Abel and Arnold Perl are the focus of this chapter. Abel’s rendition, the most widely read, believes that a bitter laugh is the only ...
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The interpretations of the story of Bontsye Shvayg by Hilde Abel and Arnold Perl are the focus of this chapter. Abel’s rendition, the most widely read, believes that a bitter laugh is the only possible climax to the story and Perl’s play, “The World Sholom Aleichem,” a dramatic rendition that has done more to bring Perets’ story before contemporary audiences, believes in Bontsye’s piety that no prosecutional laugh could challenge. The chapter presents a “wrong” interpretation of Bontsye that goes against what the text plainly expresses. It notes, however, that an interpretation is only wrong from one’s perspective because of historical factors (i.e. Holocaust) which have been a huge influence in transforming the “wrong” interpretation into what has to be right. The discussion of a “sincerely wrong” approach to Bontsye moves back to the larger issue on how to explain the contrapuntal structure of the book of Job. The chapter also mentions Ecclesiastes, whose pietistic terms must be rethought, still worked to mold the canonical shape of the book of Job.Less
The interpretations of the story of Bontsye Shvayg by Hilde Abel and Arnold Perl are the focus of this chapter. Abel’s rendition, the most widely read, believes that a bitter laugh is the only possible climax to the story and Perl’s play, “The World Sholom Aleichem,” a dramatic rendition that has done more to bring Perets’ story before contemporary audiences, believes in Bontsye’s piety that no prosecutional laugh could challenge. The chapter presents a “wrong” interpretation of Bontsye that goes against what the text plainly expresses. It notes, however, that an interpretation is only wrong from one’s perspective because of historical factors (i.e. Holocaust) which have been a huge influence in transforming the “wrong” interpretation into what has to be right. The discussion of a “sincerely wrong” approach to Bontsye moves back to the larger issue on how to explain the contrapuntal structure of the book of Job. The chapter also mentions Ecclesiastes, whose pietistic terms must be rethought, still worked to mold the canonical shape of the book of Job.
Conrad Bessant, Darren Oakley, and Ian Shadforth
- Published in print:
- 2014
- Published Online:
- April 2014
- ISBN:
- 9780199658558
- eISBN:
- 9780191779466
- Item type:
- book
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199658558.001.0001
- Subject:
- Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Biochemistry / Molecular Biology
This book provides an 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 ...
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This book provides an 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. The book is intended to provide the reader with the knowledge and confidence needed to create databases, to write programs to analyse and visualise data, and to develop interactive web-based applications. Platform-independent examples are provided throughout, making the book suitable for users of Windows, Mac OS or Linux.Less
This book provides an 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. The book is intended to provide the reader with the knowledge and confidence needed to create databases, to write programs to analyse and visualise data, and to develop interactive web-based applications. Platform-independent examples are provided throughout, making the book suitable for users of Windows, Mac OS or Linux.
Geoff Cox and Adrian Ward
- Published in print:
- 2008
- Published Online:
- August 2013
- ISBN:
- 9780262062749
- eISBN:
- 9780262273343
- Item type:
- chapter
- Publisher:
- The MIT Press
- DOI:
- 10.7551/mitpress/9780262062749.003.0029
- Subject:
- Society and Culture, Media Studies
This chapter describes the concept of Practical Extraction and Report Language (Perl), a programming language tailored with the help of shell or awk programming. The beginning of the chapter explains ...
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This chapter describes the concept of Practical Extraction and Report Language (Perl), a programming language tailored with the help of shell or awk programming. The beginning of the chapter explains the early history of Perl and continues the exploration with the naming convention of this concept. The chapter explores the reasons of Perl's representation as the interpreted scripting language and the first postmodern computer language with illustrations. Furthermore, it discusses the role of code work in Perl and explains that programming with Perl emphasizes materiality conditions.Less
This chapter describes the concept of Practical Extraction and Report Language (Perl), a programming language tailored with the help of shell or awk programming. The beginning of the chapter explains the early history of Perl and continues the exploration with the naming convention of this concept. The chapter explores the reasons of Perl's representation as the interpreted scripting language and the first postmodern computer language with illustrations. Furthermore, it discusses the role of code work in Perl and explains that programming with Perl emphasizes materiality conditions.
Conrad Bessant, Darren Oakley, and Ian Shadforth
- Published in print:
- 2014
- Published Online:
- April 2014
- ISBN:
- 9780199658558
- eISBN:
- 9780191779466
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199658558.003.0003
- Subject:
- Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Biochemistry / Molecular Biology
This chapter provides an introduction to programming for beginners, using the Perl programming language and various add-on modules. Key concepts are covered, from basic syntax and control structures ...
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This chapter provides an introduction to programming for beginners, using the Perl programming language and various add-on modules. Key concepts are covered, from basic syntax and control structures all the way through to regular expressions, database connectivity, and object-oriented programming. Numerous example programs are given, mostly taken from the world of bioinformatics.Less
This chapter provides an introduction to programming for beginners, using the Perl programming language and various add-on modules. Key concepts are covered, from basic syntax and control structures all the way through to regular expressions, database connectivity, and object-oriented programming. Numerous example programs are given, mostly taken from the world of bioinformatics.
Conrad Bessant, Darren Oakley, and Ian Shadforth
- Published in print:
- 2014
- Published Online:
- April 2014
- ISBN:
- 9780199658558
- eISBN:
- 9780191779466
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199658558.003.0005
- Subject:
- Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Biochemistry / Molecular Biology
This chapter gives a practical introduction to the development of web applications using Perl and the Mojolicious web framework. Key web technologies are introduced, including HTML5, cascading ...
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This chapter gives a practical introduction to the development of web applications using Perl and the Mojolicious web framework. Key web technologies are introduced, including HTML5, cascading stylesheets (CSS), and JavaScript. The use of these technologies in building interactive web applications is demonstrated using biologically relevant examples.Less
This chapter gives a practical introduction to the development of web applications using Perl and the Mojolicious web framework. Key web technologies are introduced, including HTML5, cascading stylesheets (CSS), and JavaScript. The use of these technologies in building interactive web applications is demonstrated using biologically relevant examples.
Conrad Bessant, Darren Oakley, and Ian Shadforth
- Published in print:
- 2014
- Published Online:
- April 2014
- ISBN:
- 9780199658558
- eISBN:
- 9780191779466
- Item type:
- chapter
- Publisher:
- Oxford University Press
- DOI:
- 10.1093/acprof:oso/9780199658558.003.0006
- Subject:
- Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Biochemistry / Molecular Biology
This chapter provides a practical introduction to key software engineering practices that can be used to facilitate the efficient production of readable, flexible, and reliable program code even in ...
More
This chapter provides a practical introduction to key software engineering practices that can be used to facilitate the efficient production of readable, flexible, and reliable program code even in complex multi-developer projects. These practices include unit testing, version control, in-code documentation, and user-centred design. The chapter also provides information on getting started with three languages that are popular in bioinformatics — Python, Ruby, and Java — and compares the capabilities of these languages with each other and with Perl.Less
This chapter provides a practical introduction to key software engineering practices that can be used to facilitate the efficient production of readable, flexible, and reliable program code even in complex multi-developer projects. These practices include unit testing, version control, in-code documentation, and user-centred design. The chapter also provides information on getting started with three languages that are popular in bioinformatics — Python, Ruby, and Java — and compares the capabilities of these languages with each other and with Perl.
