BioMart Workshop - GMOD Europe 2010

Jump to: navigation, search
GMOD Europe 2010
BioMart Workshop
16 September 2010
Cambridge UK
Part of GMOD Europe 2010

BioMart: Mining genomic data

BioMart provides a single point of access to various 'omics and annotation from disparate data sources, including biomolecular sequence resources, pathways, protein interaction and annotation. This one-day workshop was aimed to biologists who may wish to learn how to programmatically integrate various sources over the web (API/webservices), introducing the latest BioMart (0.8) Java libraries that supersedes the current Perl infrastructure. The hands-on primarily focused on the resources currently available at the BioMart Central Portal (Ensembl, UniProt, PRIDE, etc.). Furthermore, a concise introduction to some of the specialised BioMart portals such as ICGC (International Cancer Genome Consortium) and mouse resources (MGI, EMMA, Europhenome, etc.) will be presented.

Participants were expected to have intermediate level experience in writing Perl or Java programs. A background in object oriented programming techniques and familiarity with databases (MySQL) would be an advantage.



Registration was free, but required, as space was limited.


The workshop was held in the Department of Genetics, room G12-G13, at the University of Cambridge.

9:00 - 9:20 Coffee/Tea
9:20 - 9:45 Introduction to BioMart and status update (by Arek Kasprzyk)
9:45 - 12:30 Hands-on training (Perl and Java)
12:30 - 13:30 Lunch break (on your own)
13:30 - 15:00 Hands-on training (Perl and Java)
15:00 - 15:15 Coffee/Tea break
15:15 - 15:30 Mouse informatics resources in BioMart (by Damian Smedley)
15:30 - 17:00 Hands-on training and open session for user feedback.

School of Biological Sciences Bioinformatics Training Facility

This event was sponsored and hosted by the School of Biological Sciences Bioinformatics Training Facility. The Bioinformatics Training Facility organises practical training for both undergraduates and postgraduates. The vast majority of their postgraduate events are open and free to all who might benefit.

The Bioinformatics Training Facility is generously providing all coffee, tea, and break snacks at no charge. Please thank Dave Judge profusely every time you see him.

Lodging and Other Logistics

See the Logistics section on the GMOD Europe 2010 page for information.