GridQTL+: High performance web-based genetic analyses for the biosciences - NeSC Participation

  • Knott, Sara (Principal Investigator)
  • Atkinson, Malcolm (Co-investigator)
  • De Koning, Dj (Co-investigator)

Project Details

Description

The project aims to provide web based QTL analysis to the genetics research community in the UK and beyond.
The web based portal provides analyses that require computation resources that are well beyond the capacity of standard desktop computers.

Layman's description

An important area of research is the analysis of the genome to find regions where variation in the genetic material (DNA) explains variation that can be observed at the individual scale.
These analyses have been popular since the nineties but the models have beome more complex and the amounts of data have increased drastically. In order to meet the computational demands oof the desk based research we have developed web based analysis of genomic data through a secure web portal.

Key findings

The portal is up and running and provides a wide variety of analysis models to identify loci affecting traits of interest. There are over 600 registered users of the software with around 1000 analyses performed per month. We have continued to introduce novel genetic models, such as for the analysis of an unstructured outbred population, and improved algorithms. We have developed an add-on to GridQTL that gives the user options to store and retrieve genetic maps within ArkDB and subsequently to interact with Ensembl to inform about structure and genes in the region of a postulated causal locus.
We have developed a version of the software for use on a cloud. For portability we have used the open source cloud middleware OpenStack, which can run on Amazon AWS but would be portable to other cloud systems and local compute clusters.
AcronymGridQTL+
StatusFinished
Effective start/end date1/05/1030/11/13

Funding

  • BBSRC: £47,926.00
  • BBSRC: £67,873.00
  • BBSRC: £625,798.00