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Bioinformatics class

This is a one semester class with 12 1-hour lessons taught by Lukas Mueller, Genevieve DeClerck and Naama Menda.

Table of contents

1. Lesson. BioInfoIntro Brief introduction to biology, computers, and bioinformatics.
2. Lesson. Introduction. Linux, Terminals, shells, basic commands.
3. Lesson. PerlIntro Perl basics: variables, control structures, subroutines, modules.
4. Lesson. PerlTextManipulation Files, text parsing and regular expressions
5. Lesson. BioPerl.
6. Lesson. AdvancedPerl: Object Oriented Perl. Moose.
7. Lesson. Relational databases and SQL, DBI and DBIx::Class
8. Lesson. Statistics using Perl and R.
9. Lesson. Ontologies.
10. Lesson. Bioinformatics tools: NCBI (web), local blast, local web blast, alignment: muscle, bwa, SAMTools.
11. Lesson. Gene expression
12. Lesson. XML Parsing using Perl
13. References

Copyright

This course material is Copyright © 2010 by Lukas Mueller and the Boyce Thompson Institute for Plant Research.