CANCELLED – EnsEMBL API, 1 hp


National course hosted by the BILS Annotation Platform, a national resource for genome annotation. The course is open for PhD students, postdocs, researchers and other employees in need of bioinformatic skills within all Swedish universities.

Application form

 

Important dates

Application open: January 16

Application deadline: February 3

Confirmation to accepted students: February 5

Responsible teachers: Marc Höppner, Andreas Kähäri

If you don’t receive information according to the dates above, contact eva.molin@scilifelab.uu.se

 

Course fee

A course fee of 1000 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner).

 

Course content

The aim of the course will be to introduce researchers to the powerful Perl-based EnsEMBL API, a programming interface that enables direct access to all data stored within EnsEMBL data bases using well-documented Perl modules and classes. You will learn about the internal organization of EnsEMBL resources through discussions of the various databases and their structure. With this knowledge, subsequent tutorials will then focus on how to develop scripts to access and efficiently mine these data – ranging from information about individual genes, genomic regions, variation data to comparative genomics.

 

Topics covered will include:

  • The EnsEMBL project
  • EnsEMBL databases and resources
  • Using the PERL API to mine EnsEMBL:
    • EnsEMBL Core (genes)
    • EnsEMBL Compara (comparative genomics)
    • EnsEMBL Variation (SNP data)

 

Entry requirements 

Command of the Perl programming language is an absolute must to participate in this course. Participants must furthermore be comfortable navigating a linux shell and should have a good working knowledge of genomics and molecular biology in order to follow the various examples discussed in the course.

Due to space constraints for the computer exercises, there is a maximum number of allowed participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.