CS4710

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CS4710

• Why Progam?

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Why learn to program?

• Utility of programming skills
• understand tools
• modify tools
• create your own
• automate repetitive tasks
• automate system tasks
• renaming files
• searching entire directories
• perform simulations

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Paradigms of programming

• imperative
• Perl
• Fortran
• C
• Python
• object-oriented
• Java
• C
• Perl
• Python
• functional
• Lisp
• Scheme

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Notable Resources

• GenBank
• www.ncbi.nlm.nih.gov/GenBank
• (Natl center for biotechnical info)
• most know sequence data
• Protein Data Bank (PDB)
• http//www.rcsb.org/pdb
• structural info of proteins
• BLAST
• alignment tool
• BioPerl module

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Why Perl?

• de facto standard for bioinformatics researchers
• BioPerl module
• especially apt for string manipulation
• ASCII text
• available for every platform
• useful for scripts
• useful for CGI-scripts (web app.)
• PERL Practical Extraction and Report Language
• relatively quick program development

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May want to also consider Python

• beginning to be used for Bioinformatics
• especially apt for string manipulation
• ASCII text
• available for every platform
• useful for scripts
• quick program development
• very clean syntax
• supports regular expressions
• via the module re
• http//www.python.org
• re module info
• biopython.org modules

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ASCII

• American Standard Code for Information Exchange
• assigns a numeric value to characters
• letters, punctuation, digits, ...
• used to help store info in computer form(binary)

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ASCII codes

• 32 is space
• 33 is !
• 48-57 are 0-9
• 65-90 are A-Z
• 97-122 are a-z
• http//www.asciitable.com
• why is ascii important to you?
• (db query results)

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Platform

• Operating system
• MS Windows
• XP
• NT
• 2000
• 98
• Unix
• Sun Solaris
• SGI
• Linux
• RedHat's Fedora distro
• SuSE distro
• Gentoo distro
• Mac OS X (based on BSD Unix)

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Operating System

• Is a layer of software running on the computers
  hardware
• Controls the hardware resources
• Determines the user interface
• remember DOS?
• Macintosh/Apple led graphical interfaces
• Application programs run on top of the OS

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Open Source Programs

• Allows one access to the original code of a
  program (vs. big business)
• Linux
• Perl
• Mozilla's web browser Firefox
• Mozilla's news and email reader Thunderbird
• Apache web server
• OSI - open source initiative
• http//opensource.org
• http//bioinformatics.org

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Writing and running a perl program

• enter source code into a file (.pl)
• save the file
• compile and run
• perl filename.pl, or
• ./filename.pl do chmod first
• make modifications and repeat if needed

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Types of debugging

• incremental programming helpful
• thorough testing
• white box
• black box
• regression
• print statements - old reliable
• actual debuggers

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Types of program errors

• syntax
• semantic (logic)
• runtime

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Windows vs Unix terminology

• file
• program source code
• data
• directory
• same as MS Windows folder
• subdirectory
• in Unix,
• . always refers to your current directory
• .. always refers to the parent directory

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Unix command chmod

• file and directory security
• changes file or directory permissions
• your perl file must be set to executable
• ls -l
• chmod ux filename.pl
• ls -l
• user/group/other r w x

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Perl Resources

• http//www.cpan.org
• comprehensive perl archive network
• OReilly sources
• http//www.perl.com/catalog/begperlbio
• http//www.perl.com
• http//www.perl.org
• We will use Perl version 5 or higher
• perl -v
• Unix command which perl
• get the binary not the source code

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Other software and info

• Use http//www.google.com
• MS Windows download and install putty
• SSH client
• security vs. Telnet and ftp
• host acme.gatech.edu
• know where to get GT computer account help
• http//www.oit.gatech.edu
• http//faq.oit.gatech.edu/cgi-bin/mainmenu?all

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Newsgroups Website

• locate some for biology, genetic research,
  bioinformatics
• set up a newsgroup email client
• http//www.mozilla.org(Thunderbird)
• set up a better browser if you like Firefox
• http//www.mozilla.org
• tabbed web browser
• The courses newsgroup
• git.cc.class.cs4710
• The course's website
• http//www.cc.gatech.edu/sweat (and click from
  there)
• also have a "swiki" or "coweb" for the class.