The Ensembl Toolkit for Big Data Access - ASHG 2015
The application system requires cookies, and the limited processing of your personal data in order to function. By applying to this course you are agreeing to this as outlined in our Privacy Notice and Terms of Use
Course Overview
Modern biological research requires a varied toolkit, specialized for data scales from single gene to gene list to whole genome. Ensembl provides such a toolkit to access genetic and genomic data for >70 species. This workshop covers different methods for accessing big and small Ensembl data, featuring the following hands-on demonstrations:
- Flexible data export using BioMart for gene lists (10min)
- Command line querying using the Ensembl MySQL server (10min)
- Scripting with Perl-API, the most flexible method (10min)
- Accessing data via REST-API, including quick lookups, scripting in different languages, and high-throughput POST access. REST-API handles <1000 queries/second to extract genomic data via programmatic database access (20min)
- Downloading complete genomic data from the Ensembl FTP site (10min)
- Using our popular Variant Effect Predictor (VEP) to annotate variants against Ensembl genes to determine the variants’ effects including SIFT and PolyPhen. We will look at a small query using the web interface and a whole-genome query using the standalone script (20min)
Participants are encouraged to bring existing questions for a Q&A session.
Workshop requirements: You must bring your laptop. Your laptop should have full battery power and must have a wireless card.
For more information please visit the meeting homepage