• Slides: [slide show] [to print]
• Exercise 1: BLASTing ESTs against a RefSeq database
• Exercise 2: Intro to X Windows with some graphical applications
• Exercise 3 (extra credit): Create a shell script combining some EMBOSS commands (starting with script at /home/george/scripts/align.csh) [solution]

• Slides: [slide show] [to print]
• Exercise 1: Retrieving and aligning a list of human-mouse orthologs [starting script] [solution]
• Exercise 2 (extra credit): Retrieving a set of genes encoding growth factors, extracting their proximal promoters, and analyzing them. [starting script] [solution]

• Slides: [slide show] [to print]
• Exercise 1: Parsing a file of multiple BLAST reports [starting script] [solution]
• Exercise 2: Manipulating a GenBank file with BioPerl and creating a PNG image [starting script] [input file] [partial output] [solution]
• Exercise 3: Setting up a web-based search script [CGI script]

• Applying for a WIBR Bioinformatics account
• Connecting to tak/hebrides and transferring files (including sources of software to do this)
• Using X windows on tak/hebrides
• Using Cygwin/X for X Windows on Tak or Hebrides
• Local biological tools: program list and help pages
• Hebrides database list: choices for local BLAST
• Tak database list: choices for local BLAST
• BLAST documentation: details about running NCBI's blastall, formatdb, and fastacmdh
• LSF Reference Guide [contents] (commands for working on the Biocomputing Linux cluster)
• EMBOSS: The European Molecular Biology Open Software Suite
• Perl modules on tak (as of Jan 2005)
• Perl modules on hebrides (as of Jan 2005)
• Image Magick: free software suite to create, edit and compose bitmap images

• Introduction to Unix (University of Wisconsin-Milwaukee)
• Rule the World with 13 UNIX Commands
• Using the Unix Operating System 1 (Lincoln Stein)
• Using the Unix Operating System 2 (Simon Prochnik)
• UNIXhelp for Users
• UNIX Tutorial for Beginners
• All Unix Commands List
• Unix Cheat sheet
• Pico (simple text editor) tutorial
• Demo commands from WIBR "Applied Bioinformatics for Biologists" class (October 2003)

• Comprehensive Perl Archive Network (CPAN modules and documentation)
• Perl.com: O'Reilly's Perl resources (including Perl download for Unix)
• ActivePerl: Perl for Windows (download and documentation)
• Perl functions
• Perl Frequently Asked Questions
• Installing Perl modules (but check first - the module may already be installed) - and you'll need to specify the PREFIX when running Makefile.PL
• Genome Informatics at CSHL: Perl basics, control structures, arrays and hashes, loops and filehandles, regular expressions, modules
• How Perl Saved the Human Genome Project (Lincoln Stein)

• BioPerl home
• BioPerl tutorial
• BioPerl "HOWTOs": tutorials about some specific modules
• BioPerl 1.4 documentation on CPAN
• BioPerl 1.4 documentation on BioPerl
• BioPerl course (Pasteur Institute)

Sample Perl scripts

• LWP::Simple: procedural LWP interface
• CGI: creating scripts with a Web interface
• CGI::Carp: handles errors in CGI scripts (very helpful for debugging)
• BioPerl's SeqIO:for sequence input/output and format conversion
• BioPerl's SearchIO: BioPerl BLAST report parser
• GD: generate bitmap graphics
• SVG: generate vector graphics
• NHGRI's BLAST: BLAST report parser