Introduction to Bioinformatics

Topics: Bioinformatics Fundamentals (Part I) 

      Introduction to the course; Overview of computing platform;
               Designing your course WWW page
               [Chap. 1; Appendix A]
               Lab: Beginner's Guide
      Introduction to Perl; Programming strategies
               [Chap. 2-3; Appendix B]
               Lab: Getting Started with Perl
      Representing and reasoning about sequence data 
               [Chap. 4]
               Lab: Analysis of Sequence Data 
      Recap of Perl constructs; Intro to searching for motifs  
               [Chap. 5]                                           
      Regular expressions and subroutines in Perl (PROSITE)
               [Chaps. 5, 6 (pp. 87-99, 104-105); Class notes]
               Lab: Practice with Subroutines and Regular Expressions                                                 
      More fun with HTML 
               Lab: Practice with Clickable Images and Forms in HTML          
               TERM PROJECT: Part #1 
      Review for Midterm





Topics: Bioinformatics Fundamentals (Part II)


      Simulating DNA sequences and mutations;  Perl constructs revisited: using modules and pass by reference
               [Chap. 6, (pp. 98-103), Chap. 7]
               Lab: Simulating a DNA Sequence by Programming Randomization
               Lab: Creating a Reusable Perl Module 
      Term project group breakout sessions
      Numerical analysis using Perl
               Lab: Practice with Numerical Analysis in Perl 
               TERM PROJECT: Part #2      
               IEEE-ACM Software Engineering Code of Ethics and Professional Practice
               [No formal class this week - search WWW for this topic; prepare to discuss & role play]
      Course/lab wrap-up; Scientific presentations of new bioinformatics tools
               Final project presentations/class judging 
               TERM PROJECT: Part #3


 Course Wrap-up

    FINAL EXAM
             

• Subroutines in MATLAB; Image analysis and medical diagnostic systems
  Lab: Introduction to Imaging in Bioinformatics (Part I)
• Bio-tool development: More on image enhancement techniques
  Lab: Introduction to Imaging in Bioinformatics (Part II)
• Performance assessment of bioinformatics tools
  [Distance Learning Module]
• The genetic code; Restriction maps; hashes and databases (REBASE)
  [Chap. 8-9]
• More on databases and HTML (inc. Access, ColdFusion)
  [Class notes]
  Lab: Practice with Hashes and Databases in Perl
• Leading university/government bioinfomatics resources (GenBank, Protein Data Bank, BLAST)
  [parts of Chaps. 10-12 + Distance Learning Module]

• On T.V. and on-line - Be sure to check out:
  • Cracking the Code of Life - View RealVideo/QuickTime movie of this NOVA special
  • NOVA Genome Website - Search for additional information, including resources
  • NOVA On-line - Search for any upcoming programs on PBS (WSRE in Pensacola)

• Visit: UWF Software Distribution Site
  • This site is helpful if you want to install Netscape and WS_FTP on your home PC. WS_FTP is a GUI-based tool thans runs under Windows for tranferring files back and forth between your home PC and and other machines.