How to take this course


This course makes use of lecture material from a three-day course that took place at EMBL-EBI in May 2013. This course is presented by Magali Ruffier from the Core team, Anja Thormann from Variation, Nathan Johnson from Regulation and Matthieu Muffato and Stephen Fitzgerald from Compara.

If you see this video icon, you will be able to watch a video of the lecture, presented in Mediasite format. (Note that these videos will only run on Google Chrome, Internet Explorer or Safari.)




This course is made up of five modules:

  1. Core
  2. Variation
  3. Regulation
  4. Compara trees
  5. Compara alignments
NotesYou can dip in and out of these modules, and pick and choose those of interest to you. However, we recommend that you start with the Core module as this provides an introduction to using the API, including how to access the documentation and how to connect to the Ensembl database.

The slides for each lecture are available as pdf files for you to study. Lecture links will open in a new tab and pdfs will open in your default pdf viewer (eg. Adobe Acrobat or Apple Preview).

The lectures are interspersed with exercises, allowing you to try out the techniques presented in the lectures. Sample scripts are provided for each of the exercises, giving an example of how you might have found the answer; remember that there's often many ways to do something - if your script is different to the sample script but still gets the correct data, then your script is correct.

This is a long course, intended to be taken over several days. The full course consists of 5.5 hours of video, with around 12-24 hours worth of exercises, depending on how quickly you are able to complete them. 

This course is not intended to teach you Perl. Here's a great introductory course on Perl to brush up. 

Find out about hosting a similar workshop at your institute.

NotesIf you would like to jump straight to a specific section in the course please use the left-hand menu to navigate.