Tool-Building in Bioinformatics

TBiB Q4/2007

BiRC / Courses / TBiB

Recent Announcements

  • Deadline for the first project set. [20/04/2007]

    The deadline for the first project is Tuesday May 16th.
  • Preliminary version of web pages available [06/03/2007]

    The initial WWW pages are ready.
  • All published announcements

About

It's a sad fact of life that most bioinformatics software packages are incompatible — if we wish to perform a number of calculations on a set of data, the output of one program never quite matches the input of the next, and although in many cases tools exist for translating one data format into another, often the translation looses information about the data. And although we often want to combine calculations in various tools, without manually inspecting the intermediate results, building a pipeline of calculations is often not immediately possible.

In this course we will see how we can use a "scripting language" such as Python to translate data formats for use with different tools, how to wrap the tools so that they can be called and controlled from scripts for easy pipelining of calculations, how we can use databases for keeping track of data, and how to build a www interface to control your program.

Prerequisites

Some familiarity with programming, in particular the Python programming language, and some familiarity with basic text processing in Python.

Schedule

Check the weekly schedule for information about each lecture.

Lectures take place:

  • Wedensday 12.15-15.00 in Coll O1, Building 1090.

First lecture is in week 15.

Literature

The main literature will be a set of lecture notes, with supplementary reading.

Projects

Each student must participate in the series of mandatory projects. Currently two projects are planned. The last project will be graded on the 13-scale and will be the final grade.

Lecturers

If you have any comments or questions related to the course, you are welcome to contact one of the lecturers: