High on the list of priorities for many enterprises and organisations is operational efficiency and the cloud is a key driving force behind this. The Cloud Infrastructure for Microbial Bioinformatics (CLIMB) project utilised a scalable open source cloud solution to allow for collaboration and data sharing between university sites and groups. Simon Thompson, Head of IT at Swansea University, tells us more.
The Cloud Infrastructure for Microbial Bioinformatics (CLIMB) is a collaboration between Warwick, Birmingham, Cardiff, Swansea, Bath, and Leicester Universities and The Quadram Institute Bioscience. The idea behind CLIMB was to bring bioinformatics capability (computing power, storage and analysis tools) to microbiologists working in UK academia. With improvements in next-generation sequencing technologies, generating genomic datasets has become easier. Many academics don’t have access to the resources that they need to perform the required bioinformatics analysis. CLIMB will provide this resource. It will also be a place for researchers to share scripts and pipelines and produce new medical breakthroughs.
The challenge
The project needed a scalable, easily accessible cloud platform to enable it to share large amounts of genome sequence data and project datasets between university sites and groups. CLIMB’s goal was to use software-based solutions and commodity hardware to simplify collaboration.
“Genomic sequencing, for example, requires huge amounts of computing power,” said Dr Thomas Connor, Co-investigator for CLIMB. “However, most microbiologists are not computer experts. CLIMB provides a platform for IT resource access to help them easily work and collaborate more quickly.
“Different universities running different systems made it very difficult to share data,” said Connor. “Collaboration was too challenging for our IT infrastructure. We know that being able to easily share resources is a great way of getting people to work together.”
The solution
The project chose to deploy RDO OpenStack as a scalable, easily accessible cloud platform and Red Hat Ceph Storage to provide scalable object storage. With this solution, CLIMB can share a large amount of genome sequence data and project datasets between university sites and groups.
The benefits
The new solution, based on RDO OpenStack and Red Hat Ceph Storage, helps customers efficiently manage exponential data growth.
Red Hat Ceph Storage provides CLIMB with object storage that is capable of meeting the large-scale storage requirements needed to help support medical breakthroughs. Designed for the cloud, Red Hat Ceph Storage can lower the cost of storing enterprise data. It does not require additional hardware investment and is flexible and scalable. This immediately helped CLIMB to manage its data growth efficiently and automatically.
“Red Hat Ceph Storage provides object storage and block storage with incredibly high performance,” said Connor. “We can use it to store copies of images on our system so that other researchers can download and use them. The features of Red Hat Ceph Storage let us share these large volumes efficiently. We’re confident that we have the storage volume we need to keep up with future generations of research data.”
The project is also able to expand globally and experience easier collaboration. “We’ve had researchers from Gambia running analysis on the system and we had teams uploading sequencing data to OpenStack and Ceph during the Ebola outbreak in Africa. This is a large-scale, remote resource that we can ship data to, from anywhere,” said Connor.
Swansea University makes up one of the key research institutes in CLIMB. We caught up with Simon Thompson, Head of IT at Swansea University, to find out more about the solution and some of its key benefits:
The CLIMB collaborative initiative – providing a secure platform for users
We chose the Red Hat technology based on the fact that it was open source and therefore we always had the open source ethos and technology to fall back on if we needed to. Additionally, it’s such a critical role we’re running now, we need to think about getting professional support. We brought in Red Hat for its knowledge, but also the way that it is amenable and able to listen to us and support the goals we set.
I think it’s about serving our community; the microbiologists. Traditionally, servers at universities were not well maintained – it was a case of putting a server under a desk and kicking it occasionally – nor were they patched. By providing an environment where more rigorous enterprise practices are applied by staff, researchers can focus on updating the machine with insurance and apps and ensuring the package management is the latest version. Then there’s the physical security of being in proper data centres in universities and the resilience of being managed by proper dedicated hardware and software teams. Keeping the solution up to date and managed by physical data centres means it’s inherently more secure.
Scalability of the solution
Both OpenStack and Red Hat Ceph Storage are horizontally scalable and it is simply a matter turning on additional resources to scale it. It scales in a very predictable manner which gives us peace of mind as we aren’t ever hit with unexpected costs.
Other areas of progression the solution enables
It has definitely enabled the science to progress. I think it’s the unhindered access to an enterprise-grade piece of IT architecture that makes a huge difference. This group of researchers across multiple universities has free access to this flexibility, power and knowledge sharing which means they can focus on writing grants and on the delivery of the actual science without worrying about IT. There’s the knowledge that it’ll be there when they need it and we’ll scale it to fit whatever demands we have at the time. The fact that 100% of the microbial genomics academic community across the UK has adopted this technology really is a testament to its importance.
Recommending Red Hat as a vendor
I would recommend Red Hat as a vendor. When things get mission-critical, we obviously had on-prem staff do it, learning the products and supporting it, but as it becomes more popular the impact on people’s research becomes quite significant. Receiving a strong level of support with a company like Red Hat who understands the product inside out is really invaluable. It is also because Red Hat is a major contributor to the source code, so it knows about any strange issues you may be experiencing and can work on a resolution quickly. We’ve only had to contact Red Hat twice, but the team has turned it around and escalated it to staff where necessary. Red Hat really understood the problem and was able to direct my engineers to a resolution very quickly. It’s this great collaborative experience where Red Hat support us with any IT project we want to undertake. We can’t wait to continue with the vendor.
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