BNF075, Programming in Bioinformatics II, 5p
This course is part of the Master's level course program in Bioinformatics and Computational Biology.
Course description: The aim of this course is to give an introduction to building bioinformatics applications with Perl, databases (e.g. SQL), and web tools. The student will learn to plan, design, and implement a comprehensive bioinformatics tool in a team. This will include resource planning and mandatory cooperation between group members, i.e. division of the project into sub-parts where team members contribute with different parts.
Course responsible person: Jari Häkkinen
Fall 2006
The course starts November 6 and ends December 1. Course location is at Department of Theoretical Physics, Sölvegatan 14A (basement level). This is NOT at Kemicentrum.
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Oligo data Tax06_oligos_55K.base (Link only works at the department.)
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Perl Objects with POD. You can download the class template with POD
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http://cbbp.thep.lu.se/~mattias/teaching/bnf072/bnf072_exercises.html (broken link) BNF072 lecture notes.
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Perl Bookshelf (Link only works at the department.)
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Subversion notes and Subversion guidelines, and the subversion book
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MySQL documentation; MySQL tutorial and the full MySQL Reference Manual. Sample file used in the tutorial pet.txt and event.txt.
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Perl DBI information; Perl DBI web site, MySQL comments on MySQL Perl API, on registering you can access Programming the Perl DBI online.
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For a short introduction to CGI scripting, use Chapter 6 in the BNF072 lectrure notes; Chapter 6.
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The dbi_simple.pl sample script.
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Sample database connection class with a config class, and script using the classes.
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Usable databases may be ACID and the Santa Cruz human genome assembly. SQL access to these databases can be provided.
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The Human Genome Project: Exploring
Our Molecular Selves
This page was created in
May, 2004.
Latest update: September 17, 2008.
©2004-2008 jari@thep.lu.se