Python for Biologists: A Complete Programming Course for Beginners (Paperback)
暫譯: 生物學家的 Python：初學者完整程式設計課程（平裝本）

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)

學習程式設計是您對研究和職業生涯最好的投資之一。《生物學家的 Python》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資訊學問題所需的技能。

為什麼要學習程式設計？


也許您看到同事們編寫程式以節省時間並處理大型數據集。
也許您的主管告訴您，您需要為下一個項目學習程式設計。
也許您在查看工作廣告時注意到有多少工作要求具備程式設計技能。

目錄



  • 在第一章中，您將學習為什麼 Python 是生物學家和初學者的好選擇。您還將學習如何為您的操作系統安裝 Python，以及如何設置您的程式設計環境，並附上所有所需免費軟體的連結。

  • 在第二章中，您將學習如何操作文本（包括 DNA 和蛋白質序列）以及如何修正程式中的錯誤。練習：計算 AT 含量，剪接內含子。

  • 在第三章中，您將學習如何從文件中讀取和寫入數據。您還將學習如何處理文件路徑和 FASTA 文件格式。練習：拆分基因組 DNA，寫入 FASTA 文件。

  • 在第四章中，您將學習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：修剪接頭序列，連接外顯子。

  • 在第五章中，您將學習如何通過創建自己的函數來使 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。

  • 在第六章中，您將學習如何編寫能夠對數據處理做出智能決策的程式，以及如何使您的程式遵循複雜的規則。練習：根據多個標準過濾基因。

  • 在第七章中，您將學習一種處理文本模式的強大工具——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：過濾存取名稱和計算限制片段大小。

  • 在第八章中，您將學習如何以高效的方式存儲大量數據，這樣可以簡化前幾章的許多程式碼。練習：將 DNA 序列轉換為蛋白質。

  • 在第九章中，您將學習如何使您的 Python 程式與現有工具協同工作，以及如何潤飾您的程式，使其準備好供其他人使用。練習：計算 k-mer，按長度對 DNA 序列進行分組。




關於作者


馬丁·瓊斯博士（Dr. Martin Jones）已經教導生物學家編寫軟體超過五年，並教授過從研究生到首席研究員的所有人員。他目前是愛丁堡大學的生物資訊學講師。

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