User:Boris/Temp/APB

Misc. Principles

• Autonomous agent
• Bioinformatics foundations
• High Performance Computing
• Cloud computing
• Data integration

Algorithms

• Dijkstras Algorithm
• Floyd Warshall Algorithm
• APB Functional annotation

Tools

• Unix (installation notes, commands, principles, pipe)
• Unix system administration (and security)
• Unix automation shellscripts, cron
• Unix wget
• Tools for the bioinformatics lab (APB, CLUSTAL, EMBOSS, PHYLIP, T-Coffee, HMMER)
• Apache (serving a local file)
• MySQL (introduction, installation, MariaDB)
  • Database example
  • Database example-join tables
  • Database example-Perl interface
  • Database example-PHP form interface
  • DBI Mac OS X installation notes
• GBrowse (installation notes, viewing annotations, LDAS installation notes, LDAS usage)

Programming

• IDE (Integrated Development Environment) (Komodo)
• Regular Expressions
• Screenscraping
• Perl (installation notes, CPAN, principles, syntax, one liners)
  • Perl basic programing
  • Perl hash example
  • Perl LWP example
  • Perl MySQL example
  • Perl MySQL introduction (DBI Mac OSX installation notes)
  • Perl OBO parser
  • Perl programming
  • Perl programming exercises 1
  • Perl programming exercises 2
  • Perl programming Data Structures
  • Perl references
  • Perl simulation
  • Perl retrieve fasta
  • Perl/MySQL example
  • Perl: Object oriented programming
  • Perl: Ugly programming
  • Perl: Using forms
• BioPerl (installation notes, programming, BP run, BP ext, tutorials)
  • BioPerl exercise alignment
  • BioPerl exercise restriction
  • BioPerl exercise signal cleavage
• PHP

Network, Web and Communication

• MediaWiki
• Web Communication
• HTML essentials
• CGI (introduction, configuring apache, executing a script, query string input)
• Network Analysis
• Network Configuration