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CS4710 Why Progam? 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 Paradigms of programming imperative Perl Fortran C

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cs4710

CS4710

Why Progam?

why learn to program
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
paradigms of programming
Paradigms of programming
  • imperative
    • Perl
    • Fortran
    • C
    • Python
  • object-oriented
    • Java
    • C++
    • Perl
    • Python
  • functional
    • Lisp
    • Scheme
notable resources
Notable Resources
  • GenBank
    • www.ncbi.nlm.nih.gov/GenBank
    • (Nat’l 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
why perl
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
may want to also consider python
May want to also consider Python
  • also extensively used for Bioinformatics
  • especially apt for “string” manipulation
    • “ASCII text”
  • available for every platform
  • useful for “scripts”, function writing, and even object-oriented style
  • quick program development
  • very clean syntax
  • supports regular expressions
    • via the module re
  • http://www.python.org
  • re module info
  • biopython.org modules
ascii
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)
ascii codes
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)
platform
“Platform”
  • Operating system
    • MS Windows
      • Vista
      • XP
      • NT
      • 2000
    • Unix
      • Sun Solaris
      • SGI
    • Linux
      • RedHat's Fedora distribution
      • SuSE distribution
      • Gentoo distribution
    • Mac OS X (based on BSD Unix)
operating system
Operating System
  • Is a layer of software running on the computer’s hardware
  • Controls the hardware resources
  • Determines the user interface
    • remember DOS?
    • Macintosh/Apple led graphical interfaces
  • Application programs run on top of the OS
open source programs
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
writing and running a perl program
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
types of debugging
Types of debugging
  • incremental programming helpful
  • thorough testing
    • white box
    • black box
    • regression
  • print statements - old reliable
  • actual debuggers - software to help you trace your code, set breakpoints, view variable values, etc
types of program errors
Types of program errors
  • syntax
  • semantic (logic)
  • runtime
windows vs unix terminology
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
unix command chmod
Unix command: chmod
  • file and directory security
  • changes file or directory permissions
  • your perl file must be set to executable
    • ls -l
    • chmod u+x filename.pl
    • ls -l
  • user/group/other & r w x
perl resources
Perl Resources
  • http://www.cpan.org
    • comprehensive perl archive network
  • O’Reilly 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
other software and info
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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