CSCI 8725 Databases for Bioinformatics Spring 2008
1. Administration
· Class meetings in EECS 3-115 at 02:30 P.M. - 03:45 P.M. on Tuesdays and Thursdays
· Instructor: John Carlis carlis@cs.umn.edu ;
5-225c EE/CSCI; 625-6092; office hour: Tuesday 1:00 - 2:00 and by appointment
2. Keeping Score
· good grooming 0% , tests 0%
· class participation 10%
· two 10 minute class lectures 20%;
Most students will talk about a
publicly available scientific database
[There are about a thousand. start here:
http://www.ncbi.nlm.nih.gov/genome/guide/human/
http://www.ncbi.nlm.nih.gov/About/tools/restable_org.html
· project: proposal 15%, presentation 15%, report 40%
· the project topic is wide open.
3. Policies
· Grades are criterion not reference based. Therefore, you are competing against a standard, not each other. So talk to each other.
· Things are due when they are due.
· Be respectful of each other.
4. Learning
· Participate in class. You will NOT be graded on whether you speak well or poorly. However, ceterus paribus, mute students generally do worse than active ones.
· You must prepare for class. I'll assume that you have read the material and thought some about it. [By being prepared you will learn more with less effort.] On the course evaluation you will report on how often you were prepared.
· Mastery doesn’t occur in ten minute units, nor does it always move forward. Read big chunks; reread in context; draw concept diagrams.
5. Approximate Schedule
Report or lecture messages and outline due 2 days before you present.
Final report due when you present
|
week |
Tuesday class |
Topic |
Readings &resources for Carlis lectures |
Stuff |
|
1 |
1/22 |
Intro |
http://www.ncbi.nlm.nih.gov/About/sitemap.html http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html |
Become familiar with NCBI |
|
2 |
1/29 |
more intro |
http://www.ncbi.nlm.nih.gov/About/primer/ |
|
|
3 |
2/5 |
Genbank |
http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
|
|
|
4 |
2/12 |
Talk on talking, PDB, SwisProt, Prosite |
http://mmb.pcb.ub.es/em/PDF/CAPITULO-6/swisprot.htm http://us.expasy.org/prosite/ |
|
|
5 |
2/18 |
Go |
|
Submit “intent” |
|
6 |
2/25 |
Microarrays |
www.affymetrix.com |
Begin student database talks |
|
7 |
3/4 |
Pathways, KEGG |
http://www.expasy.org/cgi-bin/search-biochem-index http://www.genome.jp/kegg/pathway.html |
Submit proposal |
|
8 |
3/11 |
Proteomics |
http://us.expasy.org/ |
|
|
|
3/17-3/21 |
Spring Break |
|
|
|
9 |
3/25 |
DBMS extensions |
TBA |
|
|
10 |
4/1 |
DBMS extensions |
TBA |
|
|
11 |
4/8 |
Prints Bind |
http://umber.sbs.man.ac.uk/dbbrowser/ www.bind.ca |
|
|
12 |
4/15 |
Attend bioinformatics symposium |
|
|
|
13 |
4/22 |
SNP |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp |
|
|
14 |
4/29 |
Student reports |
|
|
|
15 |
5/6 |
Student reports |
|
|