Aug 30-Sept 5

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Return to Bioinformatics

Summary for Week 1

Chapters 1-3 of Beginning Perl for Bioinformatics

These chapters introduced the field of bioinformatics and why Perl is a good choice of programming languages for tackling topics in this discipline. Bioinformatics is defined as "the application of computational tools and techniques to the management and analysis of biological data." The book's goal is to teach programming skills and then immediately apply them to biological areas.

Benefits of Perl:

  • has features that simplify common bioinformatics tasks
  • less complicated code (can write quickly)
  • easily transfers between different computer systems
  • fairly decent speed
  • relatively easy maintenance

Perl has many modules that are kept in open-access databases like CPAN. These modules can be easily modified to meet specific needs without requiring the researcher to produce the program from scratch.

On overview of the programming process:

  • 1) Identify required inputs
  • 2) Make overall design (algorithm)
  • 3) Decide how outputs will print (files, graphs, etc)
  • 4) Rewrite algorithm in more detail (pseudocode)
  • 5) Write the Perl program code (include DETAILED comments)

Chapter 1 of Bioinformatics for Dummies "Finding Out What Bioinformatics Can Do for You" gave us a general overview of the interrelatedness and importance of informatics and biology. In addition, this chapter provided a general biology background and it also addressed the type of questions bioinformatics can help you answer.