laboratory informatics
Earlham Institute creates dedicated HPC cluster
E
arlham Institute has created a dedicated HPC cluster for international data portal ‘CyVerse’ that will provide free open-source
genome analysis for big data research. As an international collaboration between
hardware and middleware engineers at EI, and support staff in the Norwich Research Park Computing Infrastructure for Science (NRP CiS) team, University of Arizona, Texas Advanced Computing Centre and Cold Spring Harbor Labs, CyVerse UK provides free, large-scale, computing facilities and data storage designed for life scientists. Lead engineer of the CyVerse UK
team, Erik van den Bergh, said: ‘Establishing the first CyVerse node outside of the US represents a vital hub in the UK for data analysis and management. CyVerse UK can provide free HPC facilities for all UK scientists as well as allowing integration of UK apps and pipelines into the wider international CyVerse ecosystem.’ ‘CyVerse provides an intuitive web
interface, Discovery Environment (DE), where scientists can upload data and run analyses’ explained van den Bergh. ‘While this resource is hosted in the
US, the DE can automatically run tools hosted in the CyVerse UK platform, giving geographical advantages to data access speed, analysis time, and data placement policy.’ CyVerse UK currently hosts two open-
source apps and a new virtual machine environment. Gwasser (Ben Ward, Clark Group) is a statistics pipeline that performs genome-wide association studies for single phenotypes. Mikado (Luca Venturini, Swarbreck Group) is a lightweight Python pipeline to identify the optimal set of data readings from multiple transcript genomics assemblies. Both apps are for the analysis and recent publication of the allohexaploid wheat genome; a crop genome that is paramount in tackling the societal challenge of global food security. Te Polymarker pipeline will soon also
be available to scientists to create efficient SNP genome assays in wheat, together with a modified ‘Tuxedo suite’ app developed by the University of Liverpool that executes a series of pipelines for RNA-seq analysis.
www.scientific-computing.com l
CyVerse hosts two apps are for the analysis and recent publication of the allohexaploid wheat genome
CyVerse UK’s robust virtualisation platform will also provide back-end data services and web hosting for the COPO and Grassroots Genomics projects. Genomics is fast becoming a ‘big data’
science as more commonplace high- throughput technologies support faster, cheaper data analysis. Tis enables scientists more complex options when analysing data, which leads to new breakthroughs as researchers can unearth previously hidden patterns and make new discoveries from biological data. However, the scientific community
struggles to take full advantage of the data generated because of a lack of computing resources, appropriate support, and technical skills. To keep up with the latest developments,
scientific researchers need to be able to store and access datasets, models, and analysis tools, which may be hosted in different global locations to facilitate international projects. Te CyVerse UK node hardware and
soſtware environment has been set up and deployed by the core CyVerse UK team (Erik van den Bergh and Alice Minotto) in the Davey Group, Tim Stitt (Scientific Computing), and NBI Scientific Computing. Te CyVerse UK project is a BBSRC-funded collaboration between the EI, University of Warwick, University of Nottingham, and the University of Liverpool.
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LABANSWER COLLABORATION WITH GOOGLE CLOUD PLATFORM
LabAnswer has announced a collaboration with Google Cloud Platform (GCP) to deliver a cloud-based informatics platform targeting life sciences users. This will build on a long-standing
relationship between LabAnswer and biotechnology organisations that are now contending with vast amounts of data characterising biological samples. Many of these experiments will contain tens of thousands of data points – and the relationships between them can be analysed with powerful computers using this new cloud service. ‘We see this initiative as a natural evolution of the original vision for LabAnswer as the leader in laboratory informatics solutions,’ commented Mark Everding, CEO and managing partner at LabAnswer. ‘LabAnswers deep understanding of science, business processes, and information technology has allowed it to become a trusted partner for its clients, providing both technical solutions and unparalleled business value.’ LabAnswer has targeted the life sciences domain for its first set of cloud-based solutions and will collaborate with partners in application areas such as automated data mining in biotechnology and pharmaceutical discovery environments. These are examples of the life science and biotechnology applications that are drastically increasing the storage and data requirements for many laboratories and research organisations. Increasingly, experiments are generating gigabytes of raw data on a single cell, environmental or patient sample and laboratories can use cloud services to reduce the burden of managing and processing data.
‘Data is one of the most valuable assets in discovery-based organisations,’ said John Conway, director of research and discovery solutions at LabAnswer. ‘However, it is an asset that can only be capitalised once the underlying knowledge has been extracted. It is this process that LabAnswer will seek to define in its cloud-based offerings.’
OCTOBER/NOVEMBER 2016 23
Credit Earlham Institute
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