Section I - Data Analysis

1. Introduction to Computers - Binary Numbers

2. We will get started with item '3' below, but early on we will have examples of prior year's student projects (Sarah Barchinger, 4:40-5:30 T 9/11; Bryan Venters, 4:40-5:30 Th 9/13; Momoko Tajiri, 3:35-4:30, F 9/14)

3. Quantification of Biochemical Data

   • Nonlinear regression

     • convergence

     • error

   • Numerical Integration

   • General purpose software 

     • NONLIN

   • Special purpose software

     • Ultrascan

     • BiaCore

     • Kinetic Analysis

     • SAXS/WAXS structures

   • Complex Error Surface

     • crystallography

     • MAD phasing

     • molecular replacement

     • refinement

4. Exam - early to mid October

Section II - Visualizing Molecules or Topic of Student Interest
(Introduction Page)

Rasmol, MDL Chime, Molmol, Pymol, SwissPdbViewer, O, etc.

mid-Oct to the end of October

Project 1 Due end of Oct or Early Nov

1. HTML - How easy it is!
2. Images
3. Forms & Scripts
   much of this was broken when the deptartment changed from
   WindowsNT to Linux for the Web server - sorry
4. JavaScripts and Frames
   
5. MDL Chime
   • learning about Rasmol
   • MDL Chime
   • gzip
   • steps for
     • overlays
     • symmetry related molecules
     • and mean structure for NMR model sets
   • another tutorial on using MDL Chime
   • MDL Chime implementation of Rasmol
6. Spreadsheets and Plotting Software - moving files around
7. Linux - an alternative operating system
   
   2003 Students - use these remaining sites for self learning if you desire.
8. Learning About RasMol

9. Learning About KineMage

10. More on HTML

11. Finding those interesting WWW sites...
    
    Section III: Project II - November to mid Dec: due Dec 13

   2004 Students - use these for self learning if desired.

1. Sequence Alignments

2. Finding sequence and structural relationships
   (Fall of 1997 material - dated)

3. Phylogenetic Trees