Tool-Building in Bioinformatics

TBiB Q4/2007

BiRC / Courses / TBiB / Weekly Schedule

Weekly Schedule

Lectures take place wedensday 12.15-15.00 in Coll O1, Building 1090.

At the lectures we will start out by talking about the material in the lecture notes, followed by a discussion of the excercises. You are expected to read the lecture notes and do as many as the exercises as you are able to before the lectures, but there will also be time at the lectures to work on the exercises.

The topic of each lecture and reading material will be listed below.

Week 1511/4Pipelining programs using Python
Lecture note: Communication with external programs in Python

Exercises: Wrapping Clustal W

Week 1618/4Extracting information from the web
Lecture note: Web-Services

Exercises: Searching NCBI

Week 1725/4R from Python
Lecture note: RPy

Week 182/5Project Week
Mandatory project 1 — the project is presented and we briefly dicuss the problems and have a short Q&A.
Week 199/5Python object persistence
Lecture note: The pickle and shelve modules.

Week 2016/5SQL Databases part 1
Lecture note: Accessing Databases

Slides
Week 2123/5SQL Databases part 2
Lecture note: Creating and Modifying Databases

Exercises: A Database of Multiple Alignments