Beginning Perl for Bioinformatics
Author: James D Tisdall
With its highly developed capacity to detect patterns in data, Perl has become one of the most popular languages for biological data analysis. But if you're a biologist with little or no programming experience, starting out in Perl can be a challenge. Many biologists have a difficult time learning how to apply the language to bioinformatics. The most popular Perl programming books are often too theoretical and too focused on computer science for a non-programming biologist who needs to solve very specific problems.
Beginning Perl for Bioinformatics is designed to get you quickly over the Perl language barrier by approaching programming as an important new laboratory skill, revealing Perl programs and techniques that are immediately useful in the lab. Each chapter focuses on solving a particular bioinformatics problem or class of problems, starting with the simplest and increasing in complexity as the book progresses. Each chapter includes programming exercises and teaches bioinformatics by showing and modifying programs that deal with various kinds of practical biological problems. By the end of the book you'll have a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to take on more advanced bioinformatics programming. Some of the later chapters focus in greater detail on specific bioinformatics topics. This book is suitable for use as a classroom textbook, for self-study, and as a reference.
The book covers:
- Programming basics and working with DNA sequences and strings
- Debugging your code
- Simulating gene mutationsusing random number generators
- Regular expressions and finding motifs in data
- Arrays, hashes, and relational databases
- Regular expressions and restriction maps
- Using Perl to parse PDB records, annotations in GenBank, and BLAST output
Interesting textbook: The Partridge and A Pear or Desserts
Spidering Hacks: 100 Industrial-Strength Tips and Techniques
Author: Kevin Hemenway
The Internet, with its profusion of information, has made us hungry for ever more, ever better data. Out of necessity, many of us have become pretty adept with search engine queries, but there are times when even the most powerful search engines aren't enough. If you've ever wanted your data in a different form than it's presented, or wanted to collect data from several sites and see it side-by-side without the constraints of a browser, then Spidering Hacks is for you.
Spidering Hacks takes you to the next level in Internet data retrieval--beyond search engines--by showing you how to create spiders and bots to retrieve information from your favorite sites and data sources. You'll no longer feel constrained by the way host sites think you want to see their data presented--you'll learn how to scrape and repurpose raw data so you can view in a way that's meaningful to you.
Written for developers, researchers, technical assistants, librarians, and power users, Spidering Hacks provides expert tips on spidering and scraping methodologies. You'll begin with a crash course in spidering concepts, tools (Perl, LWP, out-of-the-box utilities), and ethics (how to know when you've gone too far: what's acceptable and unacceptable). Next, you'll collect media files and data from databases. Then you'll learn how to interpret and understand the data, repurpose it for use in other applications, and even build authorized interfaces to integrate the data into your own content. By the time you finish Spidering Hacks, you'll be able to:
Aggregate and associate data from disparate locations, then store and manipulate the data as you like
Gain a competitive edge in business by knowing whencompetitors' products are on sale, and comparing sales ranks and product placement on e-commerce sites
Integrate third-party data into your own applications or web sites
Make your own site easier to scrape and more usable to others
Keep up-to-date with your favorite comics strips, news stories, stock tips, and more without visiting the site every day
Like the other books in O'Reilly's popular Hacks series, Spidering Hacks brings you 100 industrial-strength tips and tools from the experts to help you master this technology. If you're interested in data retrieval of any type, this book provides a wealth of data for finding a wealth of data.
Table of Contents:
| Credits | ||
| Preface | ||
| Ch. 1 | Walking Softly | 1 |
| Ch. 2 | Assembling a Toolbox | 21 |
| Ch. 3 | Collecting Media Files | 99 |
| Ch. 4 | Gleaning Data from Databases | 141 |
| Ch. 5 | Maintaining Your Collections | 349 |
| Ch. 6 | Giving Back to the World | 363 |
| Index | 391 |
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