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

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 Initially this was via the QTL Express resource, which was recently superseded by the GridQTL resource.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.

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