Plant and Animal Genome XXV Conference

January 13 - 18, 2017

4338

Genestack - Applying High-throughput Bioinformatics Technologies to Crop Reserach

Genestack platform provides an enterprise-level infrastructure for bioinformatics R&D, with a strong focus on data and metadata management, absolute reproducibility and governance, as well as scalable computing and visualisations. It can run anywhere: on and off the cloud. Genestack has been working with Rothamsted Research, a leading UK agricultural research institute, on integrating their Ondex/KnetMiner agrigenomics suite of tools. This will enable scientists to use high-throughput bioinformatics technologies to accelerate genomics-based crop improvement and protection. Ondex allows users to build genome-scale knowledge networks: networks that integrate multi-omics datasets including ontologies, homologies, and scientific literature. KnetMiner is a tool for mining networks for specific traits. It ranks genes by different types of evidence. The discoveries can be explored using powerful network analytics and visualisations. These tools have until now been underappreciated due to high usability and technical barriers: users are limited to domain experts with access to adequate infrastructure. By integrating them into Genestack, users now have access to a simple, streamlined process from data collection, knowledge network building, to knowledge discovery. In this workshop, we will provide an overview of Ondex/KnetMiner, and its application to find candidate genes for breeding success traits in Cicer arietinum (chickpea) and Brassica oleracea (kale, cabbage, etc). Then, we’ll showcase how users can easily build, combine, explore and share their own knowledge networks in Genestack, and how the results of other Genestack analytical pipelines can be integrated seamlessly to aid discovery. Lastly, we’ll present ideas of integration with NDEx (Network Data Exchange).