Tool-Building in Bioinformatics

TBiB Q4/2006

BiRC / Courses / TBiB / Weekly Schedule

Weekly Schedule

Lectures take place thursdays 9.15-12.00 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.

Any examples from the lecture notes that are shown at the lectures can be found here

Week 14April 6.Pipelining programs using Python
Lecture note: Communication with external programs in Python

Exercises: Wrapping Clustal W

Extra material from lecture
Week 16April 20.Extracting information from the web
Lecture note: Web-Services

Exercises: Searching NCBI

Week 17April 27.Project Week
Mandatory project 1 — the project is presented and we briefly dicuss the problems and have a short Q&A.
Week 18May 4.SQL Databases part 1
Lecture note: Accessing Databases

Slides
Week 19May 11.SQL Databases part 2
Lecture note: Creating and Modifying Databases

Exercises: A Database of Multiple Alignments

Slides
Week 20May 18.Making WWW interfaces
Lecture note: CGI Scripts

Exercises: CGI Interface to Clustal W

Slides, Example
Week 22June 1.Presentation and discussion of exam project