Sirkka-Liisa Varvio and Ilari Scheinin
The course is 582604 by the Department of Computer Science, 4cu, tailored for the MBI-programme
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:
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