Practical course in biodatabases, spring 2010

Lecturer

Sirkka-Liisa Varvio and Ilari Scheinin

The course is  582604 by the Department of Computer Science, 4cu, tailored for the MBI-programme
http://www.cs.helsinki.fi/bioinformatiikka/mbi/courses/09-10/biodb

Lectures: 21. Jan - 25. Feb, Thu and Fri 14-16 in BK107

Computer class sessions: 28. Jan - 25. Feb Thu 16-18 in B221

Exam: Thu 4. March, 16-19 in B221

Contents and grading

Part 1: Weeks 1, 2, 5 , Sirkka-Liisa Varvio

Biological databases and their www interfaces. Homework-set which gives 10 points to final grade:

Part 1_Homework_set.pdf, to be submitted 19. Feb to Workshop page

Thu 21. Jan: Course introduction
                     Guest lecture: Laura Langohr Biomine.pdf

Fri 22. Jan: Computer class session (class C128) for those students who don´t have previous touch with sequence databases and BLASTing.

Thu 28. Jan: Introduction to databases, Useful reviews: NCBI database resources.pdf, EMBL EBI database resources.pdf, GenBank.pdf,
                                                                              GO.pdf, UniProt.pdf, Pfam.pdf, Ensembl.pdf, KEGG.pdf,
Thu 28. Jan: Computer class session: Exercise 1.pdf

Fri 29. Jan: Results from Exercise 1 

Fri 19. Feb: Results from Part 1 Homework set 

Part 2: Weeks 3, 4, 6 , Ilari Sceinin

Programmatic access to biological databases. Concepts of relational databases and SQL language. Python language will be used.

Relational databases, material here:  http://www.cs.helsinki.fi/u/ischeini/biodb/

Homework which gives 20 points to final grade.

In addition to 10 + 20 point homeworks, computer class sessions include exercises which must be performed (unless otherwise informed)

Exam 30 points (graded 1-5) + 30 points from homework (part 1: 10 + part 2: 20) give the total grade

Workshop page

http://wiki.helsinki.fi/display/mathstatKurssienLisasivut/Practical+course+in+biodatabases%2C+spring+2010