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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, very simple shell scripts.
3. Lesson. PerlIntro Perl basics: variables: scalars, lists, and hashes.
4. Lesson. PerlIntro2 Control structures, subroutines, modules.
5. Lesson. PerlTextManipulation Files, text parsing and regular expressions
6. Lesson. PerlUsefulModules Some useful built-in and CPAN Perl modules
7. Lesson. BioPerl.
8. Lesson. AdvancedPerl: Object Oriented Perl. Moose.
9. Lesson. Statistics using Perl and R.
10. Lesson. Bioinformatics tools: NCBI (web), local blast, local web blast, alignment: muscle
11. Lesson. bwa, SAMTools, velvet, mira, cabog.
12. Lesson. Relational databases and SQL, DBI (and DBIx::Class)

1. References

Copyright

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