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Practical course in biodatabases, spring 2010


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:

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

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

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