CS201 - Introduction to Computational Science for the Life Sciences


CS201 SYLLABUS

RESOURCES

  • Documentation for Perl programming language.

  • Resources for use with the Solaris machines, including ssh clients, timers, etc.

  • X-Windows client for viewing UNIX/Linux XWindow displays

  • Secure copy client (scp) for Windows

  • The following files are in the Portable Document Format (PDF). To view them, you will need a PDF viewer. Free viewers:
    Adobe Acrobat Reader
    Ghostscript, Ghostview, and GSview

    • LECTURE NOTES & LAB

    1/27 - Syllabus / Introduction to Bioinformatics/Programming
    Lab #1 - Higher Order Thinking Skills Test

    2/03 - Introduction to Programming
    Activity #1 - DNA to RNA Transcription
    Lab #2 - Introduction to Unix / Perl

    2/10 - Perl Program Syntax
    Activity #2 - Creating cDNA from mRNA
    Lab #3 - Writing a Perl Program/More Unix

    2/24 - More Perl Program Syntax
    Activity #3 - Finding/Counting Motifs
    Lab #4 - Practice Writing Perl Code

    3/03 - Even More Perl Program Syntax
    Activity #4 - Finding/Counting Motifs
    Lab #5 - Practice Writing Perl Code
    Lab #5 Solution - motifs_sub.pl

    3/10 - Randomization and Hash Tables / Review
    Activity #5 - Programming Mutations
    Lab #6 - Student Biology Workbench
    MIDTERM - How alike are they?

    3/17 - Student Biology Workbench
    Activity #5 - Compare our program with text's version - mutation_text.pl
    Lab #7 - continuation of Student Biology Workbench

    3/31 - Genbank/BLAST
    Activity #6 - Parsing Genbank data
    Activity #6 Solution - class_annotation.pl
    Lab #8 - Visit National Center for Biotechnology Information

    Review Book's Genbank Parsing - annotate.pl
    4/07 - Protein Data Bank
    Activity #7 - Parsing Protein Data Bank data
    Lab #9 - Visit Protein Data Bank

    4/14 - Finish Protein Data Bank Activities

    4/21 - Beginning Web Programming - HTML
    Activity #8 - Parsing Protein Data Bank data
    Lab #10 - Visit Protein Data Bank

    4/28 - No Class / General Help
    4/30 - University of Texas Health Science Center in San Antonio Presentation
    http://www.biochem.uthscsa.edu

    5/05 - Writing Perl and HTML - CGI scripts
    Activity #9 - Review/Write CGI script
    Lab #11 - Help/Review
    FINAL - Putting together a website

    ASSIGNMENTS

    DUE 2/03 - Read Chap. 1-3 - Beginning Perl for Bioinformatics
                     Assignment #1 - Bioinformatics/Computational Biology Paper
    DUE 2/24 - Read Chap. 4-5 - Beginning Perl for Bioinformatics
                     Assignment #2 - Transcription of Gene to Protein
    DUE 3/17 - Read Chap. 6-8 - Beginning Perl for Bioinformatics
                     Assignment #3 - Finding Motifs in DNA or Protiens
    DUE 4/21 - Read Chap. 10-12 - Beginning Perl for Bioinformatics
                     Assignment #4 - Gathering Data from Data Banks