Survey (Please e-mail back to Mark.Gerstein@yale.edu )

rough schedule

In-class Presentation Assignment

• 20 minute talks to be given in class (see schedule above)
• Web Page (HTML document) of the talk
• Last Year's Talks (some information wrong!): http://bioinfo.mbb.yale.edu/course/projects
• Rehashing in a different voice one of the major subjects touched on
  1. alignment methods (sequence & structure)
  2. scoring statistics (sequence & structure)
  3. protein geometry (surfaces and volumes)
  4. databases (theory & applications)
  5. genomics

"Hello World" in HTML

• Create the file sample.html in your public_html directory on pantheon. (For instance, pantheon:~mg269/public_html/sample.html.)
• This is viewed by Netscape using a URL like http://pantheon.yale.edu/~mg269/sample.html
• Here is a Minimal Sample Web Page. (View Source to see what it looks like or look at sample.txt.)
• For next week, change the heading (i.e. Main Idea) to say something else. E-mail in the URL (or just send the whole page as an attachment, if you know how).
• Be sure to copy images. Use Relative Links to make things transportable.
  • <A HREF=part2.html>Part 2</A>
    rather than
    <A HREF=http://pantheon.yale.edu/~mg269/part2.html>Part 2</A>
• Also, make sure you're comfortable with PDF. Can also send me a link to a single PDF file for final project or talk.
• http://www.csb.yale.edu/people/core/pjf/templates -- Templates for Presentations
• The ee101 page that gives instructions on how to set up a web page is
  at http://www.yale.edu/ee101/book/node2.html
  

e-mail

• e-mail via course@bioinfo2.mbb.yale.edu
• Hypertext archive of course messages
• Plaintext archive of course messages

Related Coures

• Russ Altman's course at Stanford.
• Doug Brutlag's course at Stanford.
• Principles of Protein Structure course at Birkbeck College

Final Project

Due

At End of Reading Period

Plan

Summarize and Review an area

Interpret and Analyze Data

Come up with a New Approach

Areas

Alignment Methods (sequence & structure)

Scoring Statistics (sequence & structure)

Protein Geometry (surfaces and volumes)

Databases (theory & application)

Also, Genomes, Pathways, Trees, Patterns, Docking, Modelling

Length

~6 pages in total (1500 words)

Format

Turn in printout + relative-link HTML document (or PDF)

Will be ported to course website and integrated with course materials.

Final URL like http://bioinfo.mbb.yale.edu/course/projects/joe-bone.

Coding?

Computer implementation and coding possible

Documentation still necessary!...

• perl, fortran, java, c....