Cambridge, United Kingdom
March 7, 2016
We have kick started our Innovate UK funded collaborative project with Rothamsted Research, a major UK agri-genomics research centre and the longest running agricultural research station in the world. Our objective is to combine the Genestack platform with tools developed at Rothamsted Research to enable scientists to use high-throughput bioinformatics technologies to accelerate genomics-based crop improvement and protection.
Over the past ten years Rothamsted Research has been developing techniques for multi-omics data and literature mining for gene networks analysis. These techniques are necessary to mine the wealth of public domain data to link traits to gene function and ultimately to understand complex crop traits and improve their yields, nutritional quality, as well as tolerance against diseases or drought. However, these tools can be difficult to set up and maintain for many users, especially in the industry. Combining public and proprietary datasets for building extended knowledge bases is particularly challenging.
To overcome such challenges, Genestack and Rothamsted have started to work closely on making these unique tools available on Genestack’s bioinformatics platform. The platform provides an enterprise-level infrastructure for bioinformatics R&D, with a strong focus on data and metadata management, secure sharing of data tools, absolute reproducibility and governance, as well as scalable computing and visualisations. With this project, scientists working in diverse research organisations will be able to take their data from raw machine output to knowledge-based networked contextual interpretation, combining private and public datasets and databases, and sharing their findings securely.
About Rothamsted’s Tools:
Rothamsted Research has developed a suite of tools called Ondex/QTLNetMiner. These are used to build genome-scale knowledge networks. The suite combines custom multi-omics datasets with public databases, including homology, ontologies, QTL databases, as well as biological pathways and the scientific literature. Comparative genomics and data mining are two powerful approaches to identify key candidate genes in silico. Users can search for trait descriptions, refined by lists of QTLs or differently expressed genes. The results include lists of genes prioritised based on different types of evidence. All the discoveries can be explored using powerful network analytics and visualisations.
Keywan Hassani-Pak, the Head of Applied Bioinformatics at Rothamsted Research said: “We are excited to be working with Genestack on this Innovate UK project. The integration of Ondex/QTLNetMiner into Genestack’s bioinformatics platform will increase the visibility of these tools and make it easier for industrial partners to access them within a secure, cloud-based framework.”
Early Access Programme
The project officially started just a few days ago. In the near future we will launch an early access programme to these tools for a small number of selected industry participants. Members of this programme will have access to preview releases of the software and will have the opportunity to help steer the project by contributing specific requirements and needs. If you are a working in applications of genomics to agriculture and want to be part of this group, please contact us.
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