Mastering Python for Bioinformatics How to Write Flexible, Documented, Tested Python Code for Research Computing
暫譯: 掌握生物資訊學的 Python

Ken Youens-Clark

Mastering Python for Bioinformatics
  • 出版商: O'Reilly
  • 出版日期: 2021-06-15
  • 定價: $3,300
  • 售價: 9.5 折 $3,135
  • 貴賓價: 9.0 折 $2,970
  • 語言: 英文
  • 頁數: 456
  • 裝訂: Quality Paper - also called trade paper
  • ISBN: 1098100883
  • ISBN-13: 9781098100889
  • 相關分類: Python、程式語言、生物資訊 Bioinformatics

    • 立即出貨 (庫存 < 3)

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商品描述

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 at 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()

商品描述(中文翻譯)

生命科學家今天迫切需要生物資訊學技能的訓練。許多生物資訊學程式的編寫質量不佳，且維護不善，通常是由從未學習過基本程式設計技能的學生和研究人員負責。本實用指南向博士後生物資訊專業人員和學生展示如何利用 Python 的最佳部分來解決生物學中的問題，同時創建有文檔、經過測試且可重現的軟體。

《Tiny Python Projects》（Manning）的作者 Ken Youens-Clark 不僅展示了如何編寫有效的 Python 代碼，還展示了如何使用測試來編寫和重構科學程式。您將學習最新的 Python 特性和工具，包括 linters、formatters、type checkers 和測試，以創建有文檔和經過測試的程式。您還將在 Rosalind 上解決 14 個挑戰，這是一個用於學習生物資訊學和程式設計的問題解決平台。

- 創建命令列 Python 程式以記錄和驗證參數
- 編寫測試以驗證重構的程式並確認其正確性
- 使用 Python 數據結構和模組（如 Biopython）來處理生物資訊學的概念
- 使用 makefiles 創建可重現的捷徑和工作流程
- 解析基本的生物資訊學檔案格式，如 FASTA 和 FASTQ
- 使用正則表達式尋找文本模式
- 在 Python 中使用高階函數，如 filter()、map() 和 reduce()

作者簡介

Ken Youens-Clark works as a Data Engineer at The Critical Path Institute where he helps partners in industry, academia, and government find novel drug therapies for diseases ranging from cancer and tuberculosis to thousands of rare diseases. His career in bioinformatics began in 2001 when he joined a plant genomics project at Cold Spring Harbor Laboratory under the direction of Dr. Lincoln Stein, a prominent author of books and modules in Perl and an early advocate for open software, data, and science. In 2014 Ken moved to Tucson, AZ, to work as a Senior Scientific Programmer at the University of Arizona where he completed a MS in Biosystems Engineering in 2019. While at UA, Ken enjoyed teaching programming and bioinformatics skills, and used some of those ideas in his first book, Tiny Python Projects (Manning, 2020), which uses a test-driven development approach to teaching Python.

作者簡介(中文翻譯)

Ken Youens-Clark 目前在 The Critical Path Institute 擔任數據工程師，協助產業、學術界和政府的夥伴尋找針對癌症、結核病及數千種罕見疾病的新型藥物療法。他的生物資訊學職業生涯始於 2001 年，當時他在 Cold Spring Harbor Laboratory 加入了一個植物基因組專案，並在 Dr. Lincoln Stein 的指導下工作。Lincoln Stein 是 Perl 語言書籍和模組的知名作者，也是開放軟體、數據和科學的早期倡導者。2014 年，Ken 移居到亞利桑那州的圖森，擔任亞利桑那大學的高級科學程式設計師，並於 2019 年完成生物系統工程碩士學位。在亞利桑那大學期間，Ken 喜歡教授程式設計和生物資訊學技能，並將這些想法應用於他的第一本書《Tiny Python Projects》（Manning, 2020），該書採用測試驅動開發的方法來教授 Python。

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