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Mastering Python for Bioinformatics: How to Write Flexible, Documented, Tested Python Code for Research Computing
vare #: 35228211

Mastering Python for Bioinformatics: How to Write Flexible, Documented, Tested Python Code for Research Computing

vare #: 35228211

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Shop Mastering Python for Bioinformatics: How to Write Flexible, Documented, Tested Python Code for Research Computing online at a best price in NORGE. 1098100883
  • 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 tools including linters, formatters, type checkers, and tests 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()
Publisher O'Reilly Media
Publication date June 15, 2021
Edition 1st
Language English
Print length 454 pages
ISBN-10 1098100883
ISBN-13 978-1098100889
Item Weight 2.31 pounds (1.05 kg)
Dimensions 7 x 1 x 9 inches (17.8 x 2.5 x 22.9 cm)

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Mastering Python for Bioinformatics: How to Write Flexible, Documented, Tested Python Code for Research Computing

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Software Development Editorial Review

**** "Mastering Python for Bioinformatics" is a comprehensive guide designed for individuals looking to enhance their programming skills in bioinformatics. The book is structured into two key sections: the first two-thirds tackle 14 representative bioinformatics challenges sourced from the Rosalind.info platform. These challenges focus on critical tasks that bioinformaticians often encounter, such as data transformation and motif identification. One notable strength of this book is its emphasis on understanding the rationale behind the coding solutions, rather than merely providing the 'how-to' instructions. This approach not only demonstrates effective coding techniques but also equips readers with knowledge about common pitfalls to avoid in their programming journey. The latter third of the book shifts towards the practical assembly of complete programs, emphasizing the creation of useful applications from bioinformatics data. This section adds significant value, illustrating the transition from solving isolated problems to developing comprehensive software solutions suited for broader use. Additionally, appendices covering testing and documentation practices enrich the reader's programming toolkit, although these sections are less centered on bioinformatics specifics. Targeted towards readers who already possess some command-line proficiency and an understanding of Python syntax, this book provides a sufficient refresher on relevant biological concepts for those with a basic background in biology or genetics. However, complete novices in either programming or biology may find it beneficial to reinforce their knowledge beforehand. In conclusion, "Mastering Python for Bioinformatics" serves as an invaluable resource for bioinformatics students and professionals alike. It is recommended as a must-have reference in any bioinformatics laboratory and is structured to support both thorough learning and practical problem-solving. **

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  • Comprehensive coverage of bioinformatics challenges.
  • Focuses on understanding the reasoning behind coding solutions.
  • Valuable for both beginner and intermediate programmers.
  • Includes practical programming applications, enhancing real-world usability.
  • Additional resources on testing and documentation.

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  • Some code examples may contain errors.

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