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Need open-access computational resources for bioinformatics? CyVerse UK is here for you

If you are a life scientist looking for access to additional computational power, virtual machines or a web hosting service, CyVerse UK can help.

April 15, 2020

Biology is increasingly a big data science, which requires access to powerful computational hardware. Through CyVerse UK, at Earlham Institute we’re ensuring bioinformatics is open to all. CyVerse UK offers cloud-based storage and data management tools, as well as access to web hosting and virtual machines - and it’s free for you to use.

Not everyone has access to the computational resources such as those here at EI. That’s why we have a National Capability in e-Infrastructure, which ensures that our computational power for bioinformatics is open to those who need it.

EI's data centre

What is CyVerse UK?

EI is home to one of the largest HPC centres of its type in Europe. As such, we’re perfectly positioned to host CyVerse UK.

The CyVerse UK Data Store is a cloud-based storage space, accessible via the CyVerse Discovery Environment (DE), a virtual bioinformatics lab workbench, and via AGAVE API, a developer API. In the DE, users can share datasets and tools to analyse data with as many or as few people as they wish. Tools to analyse data developed by CyVerse and CyVerse UK staff or built by users can be shared with the wider community, in a similar manner to ‘apps’ on smartphones.

CyVerse UK allows users to readily store, annotate, and analyse their data, supporting a wide range of research projects. These include genome-wide association studies exploiting natural variation in crops, predicting biological networks and pathways, and high-throughput imaging and image analysis services that are bridging the genotype to phenotype gap.

Importantly, CyVerse UK can enable UK researchers to access extensive data storage and back-up, local and global compute power, and structured, integrated analysis applications and workflows.

How can I use CyVerse UK? Access virtual machines

Are you looking for additional computational power or a full Linux environment for development and analyses? Any life science researcher in the UK who wants to access a virtual machine (VM) for either web hosting or to run analyses can get in touch with the team to discuss their requirements.

Some feedback from recent users:

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The experience with setting up CyVerse resources has been very positive overall, in particular it's good to have direct contact with experts in IT.

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I could do everything I needed [...], I didn’t try compiling but assume it would work if needed.

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I’m a developer looking to share my software as open access

If you’re a developer, you could host your application on CyVerse UK.

Many applications and tools often remain in prototype form, for use only within the group or laboratory that generated them, because there is comparatively little standardisation and no easy means of sharing an accessible, user-friendly version of the tool. Through wrapping such applications in Docker containers, the CyVerse UK team is ensuring that applications can live long after a project reaches the end of its funding cycle - and can be used by the wider research community.

If you are interested in sharing your software as an open access application, again you can contact the CyVerse UK team here.

Services powered by CyVerse UK

A number of bioinformatics and data management services are also powered by CyVerse UK, made available through Earlham Institute’s National Capability in e-Infrastructure.

Applications include:

  • Grassroots Genomics - a platform that enables ”consistent approaches to generating, processing and disseminating public wheat datasets”
  • COPO - An easy-to-use ‘big data broker’ which allows users to easily keep track of, and manage, metadata, ensuring that data is easily reusable, shareable and properly attributed.
  • Galaxy - easy web-based access to the most common bioinformatics tools for genomics, transcriptomics, phylogenetics and more
  • Knetminer - “a platform to make biological knowledge discovery faster and fun”

A number of other applications are currently being integrated into the service and will be made available. These include tools for systems biology and network analysis.

Article author

Peter Bickerton

Scientific Communications & Outreach Manager