GENOMICS & PROTEOMICS
third-party open-source tools such as Ensembl, and
designing/implementing/executing data analysis pipelines for processing information such as NGS data or other genomic datasets in order to discover new biomarkers, targets, and so on.
“The third-party installations are required by customers who do not necessarily have the time to do it themselves or who struggle with the installation process due to poor-quality documentation or support from the original developers,” says Holland “We also do a lot of work integrating these third-party tools into internal systems and with internal data. A large proportion of our work is done on the Amazon cloud but we can also work on existing in-house hardware at customer sites. All work is carried out on a fixed-cost project basis where possible.
“Where it is not possible to fully define requirements, we are able to offer a flexible time-and-materials approach as an alternative. We prefer to work on projects that are large, more likely to be long-term, and of a diverse nature in order to maintain our exposure to as wide a section of genomic research as possible. Smaller one-off projects are useful as leads into longer-term relationships.
“Our typical customer is a large multinational biotechnology organisation. Examples include Big Pharma, consumer goods companies working with biological material, seed producers, veterinary medicine, animal feed producers, fuel companies researching biofuels, and so on. We work for nine out of the top ten Big Pharma and typically have about four or five projects on the go at any one time,” he says.
Case study: reaching a commercial market
One example of Eagle’s capabilities is provided by Taverna, a software project by the University of Manchester, the output of which is a tool for designing automated data processing and analysis pipelines. The University of Manchester recently published a case study about how collaborating with Eagle Genomics has allowed the Taverna project to reach a wider commercial market: “This case study was a description of how the University trained Eagle to become experts in using and deploying Taverna, so that Eagle would then be able to provide commercial support to anyone using the tool,” Holland explains “The agreement was set up in such a way that any commercial work that Eagle subsequently got involved in that required the use of Taverna would see a portion of revenue returned to the project to support its further
development.
“It benefits the commercial market by allowing commercial users of Taverna to be able to obtain commercial-grade support agreements around it from Eagle, thus enabling it to be put to better use in production environments where access to support under a service level agreement (SLA) is vital.”
Eagle has a similar arrangement with the Ensembl genome browser project team at the EBI, and with the TraitTag team at the John Innes Centre: “The relationships with these software project teams are not projects in themselves and so do not typify anything. However, they show our support for the open- source community and our willingness to participate and play an important role in ensuring the sustainability and ongoing development of the open-source tools that we use in our day-to-day work with customers,” says Holland.
‘Into the cloud’
Eagle can help customers plan, pilot and migrate their existing bioinformatics systems ‘into the cloud’, for example, a customer might have an existing bioinformatics software system running on in-house hardware, which has been the traditional approach to date. Eagle can help such a customer implement an equivalent system on top of cloud services such as Amazon Web Services. This is advantageous because the cloud is much more scalable than companies’ in-house resources, and can offer much more compute resource which might be able to speed up their research by running their software faster:
“Depending on the situation, it can also be cheaper to run their software in the cloud than to purchase or hire dedicated in-house IT infrastructure to support it,” says Holland. “Whilst still at the early stages, it is becoming increasingly common for customers to investigate this option. Bioinformatics in particular is a common candidate for such experimentation with the cloud as the size of the data involved often makes existing infrastructure struggle.
“The hurdles remain largely in the realm of legal and compliance, where existing regulations and policies have not necessarily kept up with the speed of IT development and are not designed to take into account the use of cloud in research activity. “Almost everything we do touches the cloud at some point. Some customers require us to use their in-house data centres where they exist and have suitable capacity, but everything else we do takes place on Amazon,” he says.
Technology-agnostic approach Holland states that Eagle’s competitive
advantage comes through the company’s technology-agnostic approach: “Unlike our competitors, we do not come to a project with an intention to somehow force an existing toolkit into a hole that it might not fit – competitors might do this in order to increase sales of that toolkit rather than completely solve the problem that the customer has. Our approach is always science-first. We find out what the research question being asked is, then we design exactly the right solution that makes use of the best technology available – whether it be open- or closed-source. “For example, in one project, Eagle helped Unilever migrate an existing in-house genomics analysis pipeline into the Amazon cloud, where it ran up to 20 times faster and allowed up to 10 times as many analyses to run simultaneously. Eagle has also helped ARK Genomics at the Roslin Institute to design and develop an analysis workflow that took Illumina NGS data from chicken embryo and mined it for novel miRNA biomarkers of interest to the researchers that commissioned the project.
“the bioinformatics and genomics sector is in rapid growth and that Eagle is well placed to keep pace with it: “NGS will enable sectors that have never previously been involved in genomics to take advantage of the technique to advance their research. In a decade’s time there shouldn’t be any major biotech research sector that will not have used NGS and its associated bioinformatics to advance the development of their products,” he states. “As far as Eagle is concerned, first-to- market will only get us so far. To stay ahead of the game, we will need to retain our perceived position as accepted experts, be scientifically savvy, flexible, and always deliver exactly what the customer needs regardless of the technology required to do so,” he concludes.
Further information Richard Holland Chief Business Officer Eagle Genomics Ltd Babraham Hall Babraham Research Campus Babraham Cambridge CB22 3AT United Kingdom Tel: +44 1223 654481 Fax: +44 1223 281125
Internet links Email:
richard.holland@eaglegenomics.com Web:
www.eaglegenomics.com
July/August 2012 sp2 Inter-Active 27
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