Bioinformatics: Ensembl API Workshops

Prerequisites

• This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website.
• The workshop covers the Core (Day 1), Variation (Day 2), Functional Genomics (Regulation) (Day3), and Compara (Day4) databases and APIs.
• Each database schema and API design will be presented in association with practical sessions in which the participants will write their own Perl scripts.
• Further information concerning course content is available.

• This course is comprised of 4 one day sessions.
• The first Core API session (or equivalent experience) is a mandatory prerequisite to the other 3 sessions.
• Please specify which of the optional sessions you wish to attend when booking. The default is "all three of them".
• Participants are requested to give us a little information about their background & requirements by registering here.
• The course fee, for those participants required to pay, will be £100 independent of the number of sessions attended.
• The course timetable can be viewed here.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

• Our courses are open to all who might benefit
• Booking priority is given to people from Cambridge University and Collaborating Institutes
• Individual Course fees are required only from External participants not from Collaborating Institutes

• A good grasp of programming concepts
• Experience in coding in PERL
• Familiarity with basic Molecular Biology and Genetics
• Familiarity with the Ensembl would be advantageous
• The Core API session is required to fully benefit from any of the other three sessions.

• Day 1: Core Database & API
• Day 2: Variation Database & API
• Day 3: Functional Genomics (Regulation) Database & API
• Day 4: Compara Database & API - Gene Trees
• Day 4: Compara Database & API - Alignments

• To enable those with some experience in both Molecular Biology and Programming to use the Ensembl APIs competently

• Presentations and practicals
• Four full day sessions in total
• One mandatory one day session plus three optional one day sessions

A recent version of this course has been recorded and is available for viewing, in part or in its entirety, from here.

4

A number of times per year

• Bioinformatics: Using the Ensembl Genome Browser
• Bioinformatics: An Introduction to Solving Biological Problems with PERL
• Software Carpentry: A Practical Introduction to Good Programming Practices