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

Lead Research Organisation: University of Edinburgh
Department Name: Sch of Biological Sciences

Abstract

Unravelling the genetic factors underlying product quality and efficiency in agriculture as well susceptibility to disease in agriculture and human medicine is an area of continued scientific interest. While we cannot yet fully describe the path from 'sequence to consequence' there is increasing literature on genome regions affecting traits of interest (quantitative trait loci or QTL). The last 5 years has seem a tremendous increase in the populations used for genome analysis, the numbers of molecular markers used (from a few hundred microsatellites to half a million SNP markers), and the type and number of phenotypes and pseudo phenotypes (gene expression using microarrays, protein yields and metabolomics). We have developed user friendly tools for genome analyses over the last decade. Initially this was via the QTL Express resource, which was recently superseded by the GridQTL resource. GridQTL offers a web based user-friendly analysis portal for QTL analyses in outbred pedigrees using the grid as a flexible computer resource to enable computationally demanding applications For the proposed GridQTL+ project we aim to add sustainability to the GridQTL resource and provide further functionality through integration with relevant databases.

Technical Summary

The GridQTL project was funded through the BEPII initiative to replace the QTL Express web service. The GridQTL resource was required to cope with larger pedigrees, increased numbers of markers and phenotypes as well as increased complexity of genetic models. The GridQTL project will finish in December 2009 with full functionality but no funds to sustain its maintenance and ongoing development. The proposed GridQTL+ project will provide sustainability to the GridQTL portal in two ways: A) In the short term the funding will secure the ongoing support of the GridQTL service. B) During GridQTL+ scenarios for user-funded maintenance of GridQTL will be explored and potentially implemented. GridQTL+ will also increase the flexibility of GridQTL in terms of exploiting computational resources allowing use of (inter)national grid or Cloud platforms as well as local multi-processor machines without any noticeable different to the user. The functionality of GridQTL will be further enhanced through integration of GridQTL with QTL databases. This will facilitate the direct, semi-automated, interrogation of relevant databases with the QTL results, removing the need for manual database queries. Furthermore, the project will keep abreast with the scientific developments in the area of QTL mapping methodology and implementing relevant new tools where this is deemed useful for the user community

Publications

10 25 50
 
Description We have further enhanced the software GridQTL. It is available globally through a web-interface and provides a wide variety of analysis models to identify genetic loci affecting traits of interest. 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 to store genetic maps and to interact with a genetic database. We have developed a version of the software for use on a cloud. One of the first working cloud services of this type.
Exploitation Route GridQTL is used to enhance knowledge of the genetic architecture of complex traits, which could be health or production related. It is available worldwide and can analyse data from many species. Knowledge gained about specific genes involved in trait control for a particular species can be incorporated into breeding programmes, possibly through introgression and selection. More general knowledge gained about the genetic architecture can be used to improve our understanding of genetic control.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Pharmaceuticals and Medical Biotechnology

URL http://www.gridqtl.org.uk
 
Description GridQTL gives biologists from both academia and industry access to a high powered genetic analysis tool to identify genes important in the expression of traits of interest. Subsequently the information is used in a wide variety of applications, such as in breeding plans for production and welfare, risk assessment of disease, aiding understanding of the processes of evolution and host-parasite interactions. These can have important impact on sustainable food production and animal welfare. CloudQTL can act as a template for other groups interested in developing cloud services.
First Year Of Impact 2011
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Pharmaceuticals and Medical Biotechnology
Impact Types Societal,Economic

 
Title GridQTL 
Description We have developed methods for the analysis of genetic data and implemented them in user friendly software providing the intensive computer resources required to run them. The GridQTL portal has been developed and is publicly available from www.gridqtl.org.uk. For security reasons and to enable user data storage and retrieval, access to the portal is via a single authenticated logon which can be requested from the GridQTL website. 
Type Of Technology Software 
Year Produced 2006 
Impact Through the GridQTL paltform we have 600 researchers worldwide who use our platform to perform genetic analyses on their own experimental data. Without this resource, many of these groups would rely on collaborators or external help. This platform has also been used widely to introduce students and young researchers to the methodology for QTL mapping. 
URL http://www.gridqtl.org.uk
 
Description JISC Roadshow 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Geographic Reach Local
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact The aim was to introduce alternative computing resources to other researchers. Afterwards there was discussion about the computing resources available and their use.

Researchers were made aware of resources available to them, the uptake and subsequent impact is difficult to gauge.
Year(s) Of Engagement Activity 2010