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Bioinformatics class

This is a one semester class with 12 1-hour lessons.

Table of contents

1. Lesson. Introduction. Linux, Terminals, shells, basic commands.
2. Lesson. PerlIntro Perl basics.
3. Lesson. Text parsing and regular expressions
4. Lesson. BioPerl.
5. Lesson. Object Oriented Perl.
6. Lesson. Relational databases and SQL, DBI and DBIx::Class
7. Lesson. Statistics using Perl and R.
8. Lesson. Ontologies.

Unix (Linux). Processes. File management. Terminals and shells (bash) shell scripts, (.bashrc). Commands, command line parameters, man pages, aliases, $PATH, environment variables. line top jobs Sed grep cut sort vi find, ftp, ssh, scp, Emacs.
Ubuntu: installation of additional programs. Aptitude. Installation of dual boot systems. Virtual machines.

1. Lession. Perl basics

Perl “hello world!\n”; variables scalars, lists, hashes, control structures, if else elsif statements foreach for keys while subroutines parameter passing, files, file handles, POD, shell and perl

1. Lesson Regular Expressions

1. Lesson bioperl

1. Bioinformatics tools

Bioinformatics tools: NCBI (web), local blast, local web blast, alignment muscle, bwa

1. Lesson. Databases, SQL, DBI, DBIx::Class

1. Lesson. Statistics in Perl and R (PDL and R)

1. Lesson Ontologies

1. Lesson Object Oriented Perl. The traditional way and the Moose way

1. Lesson XML Parsing using Perl

8)PDL, R
10)Gene expression,
11)ontologies (Gene Ontology and Plant Ontology and Trait Ontology)
12)NCBI PFAM Gramene
13)Object oriented Perl (Moose?)
14)Python?

Good examples:
BLAST: parameters, parsing blast files (m8), fastacmd, formatdb, blast programs: blastn, …, psi-blast, megablast, etc.

muscle