Computational Biology, 2nd Edition

Book Description

Computational Biology: A Practical Introduction to BioData Processing and Analysis with Linux, MySQL, and R

This greatly expanded 2nd edition provides a practical introduction to

• data processing with Linux tools and the programming languages AWK and Perl
• data management with the relational database system MySQL, and
• data analysis and visualization with the statistical computing environment R

for students and practitioners in the life sciences. Although written for beginners, experienced researchers in areas involving bioinformatics and computational biology may benefit from numerous tips and tricks that help to process, filter and format large datasets. Learning by doing is the basic concept of this book. Worked examples illustrate how to employ data processing and analysis techniques, e.g. for

• finding proteins potentially causing pathogenicity in bacteria,
• supporting the significance of BLAST with homology modeling, or
• detecting candidate proteins that may be redox-regulated, on the basis of their structure.

All the software tools and datasets used are freely available. One section is devoted to explaining setup and maintenance of Linux as an operating system independent virtual machine. The author’s experiences and knowledge gained from working and teaching in both academia and industry constitute the foundation for this practical approach.

Table of Contents

Part I Whetting Your Appetit
1 Introduction
2 Content of This Book

Part II Computer and Operating Systems
3 Unix/Linux

Part III Working with Linux
4 The First Touch
5 Working with Files
6 Remote Connections
7 Playing with Text and Data Files
8 Using the Shell
9 Installing BLAST and ClustalW
10 Shell Programming
11 Regular Expressions
12 Sed

Part IV Programming
13 AWK
14 Perl
15 Other Programming Languages

Part V Advanced Data Analysis
16 Relational Databases with MySQL
17 The Statistics Suite R

Part VI Worked Examples
18 Genomic Analysis of the Pathogenicity Factors from E. coli Strain O157:H7 and EHEC Strain O104:H4
19 Limits of BLAST and Homology Modeling
20 Virtual Sequencing of pUC18c
21 Querying for Potential Redox-Regulated Enzymes

Appendix A Supplementary Information

中文：

书名：Computational Biology, 2nd Edition

计算生物学：使用Linux、MySQL和R进行生物数据处理和分析的实用介绍

这一大大扩展的第二版提供了一个实用的介绍

• 使用Linux工具和编程语言AWK和Perl进行数据处理
• 使用关系数据库系统MySQL进行数据管理，以及
• 利用统计计算环境R进行数据分析和可视化

面向生命科学领域的学生和从业者。虽然是为初学者编写的，但涉及生物信息学和计算生物学领域的经验丰富的研究人员可能会从帮助处理、过滤和格式化大型数据集的许多提示和技巧中受益。在实践中学习是本书的基本理念。工作示例说明了如何使用数据处理和分析技术，例如

• 在细菌中发现可能导致致病的蛋白质，
• supporting the significance of BLAST with homology modeling, or
• 根据其结构检测可能受氧化还原调节的候选蛋白质。

所有使用的软件工具和数据集都是免费提供的。有一节专门解释了Linux作为独立于操作系统的虚拟机的设置和维护。作者在学术界和产业界的工作和教学中获得的经验和知识构成了这一实用方法的基础。

目录表

Part I Whetting Your Appetit
1 Introduction
2 Content of This Book

第二部分计算机和操作系统
3 Unix/Linux

Part III Working with Linux
4第一次接触
5 Working with Files
6 Remote Connections
7处理文本和数据文件
8使用外壳
9安装BLAST和Clusta W
10壳牌编程
11 Regular Expressions
12 Sed

第四部分方案编制
13 AWK
14 Perl
15 Other Programming Languages

Part V Advanced Data Analysis
使用MySQL的16个关系数据库
17 The Statistics Suite R

Part VI Worked Examples
18大肠杆菌O157：H7株和EHEC株O104：H4致病因子的基因组分析
19 BLAST和同源建模的局限性
20 pUC18c的虚拟测序
21查询潜在的氧化还原调节酶

附录A补充资料