Bioinformatics software development and Perl programming

Perl programming's courses are an overall introduction to the programming bases and to Perl's application in the Bioinformatics field. Courses do not require previous knowledge on programming languages. We will encourage students to explain their own requirements in this field to try to solve, at the end of the course, their specific needs. The recommended course's duration is between 15 and 20 hours.

RECOMENDED PROGRAM:

  • Perl's programming for the resolution of Bioinformatics problems
    • Brief introduction to Bioinformatics
    • The data integration problem
    • External data sources
    • Local data bases
    • Screen scraping vs. Web services and standardised formats
    • Why Perl?
  • Programming strategies
  • Example to develop: local management system for biological information
  • Perl's language
    • Features
    • Programming tools
    • Installation
  • Types of variables in Perl
    • Scalar variables and operations with scalars
    • Matrices (arrays) and operations with matrices
    • Associatives matrices (hashes)
  • Sequences and strings
    • Getting in and out from the program
    • Commands and basic operations
    • Lectura i escriptura d'arxius
  • Fluc control
    • Conditional instructions
    • Operators
    • Loops
  • Regular expressions and pattern matching
    • Pattern matching
    • Meta-characters
    • Pattern extraction
    • String replacement
  • Subroutines and modules
    • Subroutines
    • Packages
    • References to variables: what they are and how they work?
  • Interaction with the system: execution of local programs
  • Internet packages, data bases and BioPerl
    • Perl's packages: what are they, where to find them and how to install them?
    • LWP: URL's access
    • DBI: connection to data bases
    • BioPerl: examples about format conversion, basic statistics, access to molecular data bases, reading files PDB, remote execution and local for Blast and Clustal
  • Next steps
  • Use of the integration example and student's specific problem resolution
Campus d'excel·lència internacional U A B