Python for Biologists: A Complete Programming Course for Beginners (Paperback)

Dr Martin Jones

Python for Biologists: A Complete Programming Course for Beginners (Paperback)

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商品描述

Learning to program is one of the best investments that you can make for your research and your career. Python for biologists is a complete programming course for beginners that will give you the skills you need to tackle common biological and bioinformatics problems.

Why learn programming?

Maybe you see colleagues writing programs to save time and deal with large datasets.
Maybe your supervisor has told you that you need to learn programming for your next project.
Maybe you've been looking at job ads and noticed just how many of them are asking for programming skills.

Table of contents

  • In chapter one, you'll learn why Python is a good choice for biologists and beginners alike. You'll also learn how to install Python for your operating system and how to set up your programming environment, complete with links to all the free software you'll need.
  • In chapter two, you'll learn how to manipulate text (including DNA and protein sequences) and how to fix errors in your programs. Exercises: calculating AT content, splicing introns.
  • In chapter three, you'll learn how to read and write data to and from files. You'll also learn how to deal with file paths and the FASTA file format.Exercises: splitting genomic DNA, writing a FASTA file.
  • In chapter four, you'll learn how to process many pieces of data in a single program and more advanced tools for sequence manipulation. Exercises: trimming adapter sequences, concatenating exons.
  • In chapter five, you'll learn how to make Python even more useful by creating your own functions, including the best ways to test those functions in order to speed up development. Exercises: Analyzing the amino acid composition of protein sequences.
  • In chapter six, you'll learn how to write programs that can make smart decisions about how to handle data and how to make your programs follow complex rules. Exercises: filtering genes based on multiple criteria.
  • In chapter seven, you'll learn an incredibly powerful tool for working with patterns in text - regular expressions - and how to use it to search in DNA and protein sequences. Exercises: filtering accession names and calculating restriction fragment sizes.
  • In chapter eight, you'll learn how to store huge amounts of data in a way that can still allows it to be retrived very efficiently. This allows simplification of much of the code from previous chapters. Exercises: translating DNA sequences to protein.
  • In chapter nine, you'll learn how to make your Python programs work in harmony with existing tools, and how to polish up your programs so that they're ready for other people to use. Exercises: counting k-mers, binning DNA sequences by length.


About the author

Dr. Martin Jones has been teaching biologists to write software for over five years and has taught everyone from postgraduates to PIs. He is currently Lecturer in Bioinformatics at Edinburgh University.

商品描述(中文翻譯)

學習程式設計是您為研究和職業生涯做出的最佳投資之一。《Python for biologists》是一門針對初學者的完整程式設計課程，將為您提供解決常見生物學和生物信息學問題所需的技能。

為什麼要學習程式設計？
也許您看到同事們正在撰寫程式以節省時間和處理大型數據集。
也許您的主管告訴您，您需要為下一個項目學習程式設計。
也許您一直在看工作廣告，並注意到有多少工作要求具備程式設計技能。

目錄


  • 第一章介紹了為何Python是生物學家和初學者的不錯選擇。您還將學習如何為您的操作系統安裝Python，以及如何設置完整的程式設計環境，包括所有所需的免費軟體連結。

  • 第二章介紹了如何操作文本（包括DNA和蛋白質序列）以及如何修復程式中的錯誤。練習：計算AT含量，剪接內含子。

  • 第三章介紹了如何從文件讀取和寫入數據。您還將學習如何處理文件路徑和FASTA文件格式。練習：分割基因組DNA，編寫FASTA文件。

  • 第四章介紹了如何在單個程式中處理多個數據片段以及更高級的序列操作工具。練習：修剪適配器序列，連接外顯子。

  • 第五章介紹了如何通過創建自己的函數使Python更加有用，包括測試這些函數的最佳方法以加快開發速度。練習：分析蛋白質序列的氨基酸組成。

  • 第六章介紹了如何編寫能夠根據數據處理方式和複雜規則做出智能決策的程式。練習：基於多個標準過濾基因。

  • 第七章介紹了一種在文本中處理模式的非常強大的工具-正則表達式-以及如何使用它在DNA和蛋白質序列中進行搜索。練習：過濾存取名稱並計算限制性酶切片段大小。

  • 第八章介紹了如何以高效檢索的方式存儲大量數據。這使得前幾章的程式碼簡化。練習：將DNA序列翻譯為蛋白質。

  • 第九章介紹了如何使您的Python程式與現有工具協同工作，以及如何改進您的程式，使其準備好供他人使用。練習：計算k-mer數量，按長度對DNA序列進行分組。

關於作者
Dr. Martin Jones已經教授生物學家撰寫軟體超過五年，並教授過從研究生到PI的所有人。他目前是愛丁堡大學的生物信息學講師。

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