Watermelons, apps, Isambard Kingdom Brunel and will big data and bigger cuts cripple bioinformatics?
The Babraham Research Campus in Cambridge recently hosted the 3rd Eagle Bioinformatics Symposium, where experts from a range of scientific and technical industries gathered to hear about the latest developments in bioinformatics.
The symposium is the only UK bioinformatics event that provides cross-sector coverage and which also appeals to industry and academics alike. Delegates heard from academia, industry practitioners and bioinformatics experts including GSK, MedImmune, J&J, Syngenta and the Naturalis Biodiversity Centre (better known as the Netherlands’ equivalent to the UK’s Natural History Museum).
The day began with a talk from Anthony Rowe, speaking on behalf of Janssen, who described eTRIKS, a public private consortium made up of pharmaceutical partners and academic centres of excellence in data management. Anthony described the current state of the project and how it was providing a hub for a growing ecosystem of open source informatics technologies.
Next up was Matthew Woodwark from MedImmune, who described how informatics was impacting biologics drug discovery and development at MedImmune. He likened the current environment to the late 1990s, and the challenges from that time, associated with small molecules.
The keynote speaker for the event was John Wise from the Pistoia Alliance, who described how the Pistoia Alliance was championing open innovation as a possible solution to the challenges faced by the pharmaceutical industry in developing new drugs.
John presented data which showed how, despite the increasing investment in pharmaceutical research and development, actual output had halved over the past decade. Using the innovative British engineer Isambard Kingdom Brunel as an example, he described how there was a need for the pharmaceutical industry to emulate his radical thinking and develop new ideas to ensure the continued discovery of new drugs. John also described the range of projects Pistoia is involved in, including HELM, a new language for describing macromolecules, the development of an app strategy to improve pre-competitive collaboration, Controlled Substances and Compliance Services, which will help pharma to maintain compliance across all geographies and transMART, a project to enable scientists to mine and analyse translational research data.
Rutger Vos from the Biodiversity Centre described how bioinformatics was becoming increasingly important in natural history, how it is helping deal with many issues, but also the challenges it is creating, such as acquiring expertise, manpower and computational resources to handle the deluge of data.
GSK’s Victor Neduva then described some of the challenges associated with high-throughput sequencing in pharma, particularly in the areas of processing, storing and archiving data. He then went on to describe some of the solutions developed at GSK to deal with these areas.
The talks then moved on to plant genomics, with Florence Servant from Syngenta talking about the challenges that marker assay development in plants is meeting as it develops to manage evolving genotyping technologies, data integration and genomics tools. Remco Ursem from Rijk Zwann followed with a talk discussing the challenges in next generation bioinformatics for vegetable breeding.
Henrik Seidel from Bayer Healthcare gave a report on the setting up of RNA sequencing in a pharma company, discussing not just the technical issues such as computing power and data storage, but also the legal issues.
Jiye Shi from UCB raised the prospect of using mobile crowd computing as a green computing resource. A team at UCB has been evaluating the computing power and energy efficiency of mobile devices and has found that a mobile-based distributed computing system is able to save 55% to 98% of the energy consumption of conventional servers while providing comparable computing speed.
The day was finished off with a talk by Katy Wolstencroft from the University of Manchester who talked about myGrid, an initiative that is intended to improve collaboration and workflows between researchers.
Feedback from the event has been extremely positive.
Glyn Bradley, a Computational Biologist at GlaxoSmithKline, said: “There was a very impressive list of analysts and speakers, from extremely diverse backgrounds and sectors. Everyone across the different industries has the same problem in terms of big data: what to do with it and how to get it in the right place to actually work on it. The biggest challenge now is moving it around and storing it. We all know how to analyse it and understand what results we want out of it at the end but physically dealing with it and storing it poses the biggest problem right now.”
Dr. Effie Mutasa-Gottgens from the National Institute of Agricultural Botany, said: “At NIAB, we generate a lot of data but I never think of it in the same way as all the same kind of second generation sequencing stuff, but actually we’re in the same predicament. Most of the data we are producing is statistical data from information that we’re collecting from phenotyping plants. There’s a lot of information and I’m not entirely sure we are storing and managing it effectively or how we access in the future.”
Alex Gutteridge, Principal Scientist at Pfizer, said: “There was a good mix of speakers. You can see how NGS is now a core part of most organisations research. The big question is how it comes across into the clinical side because it tends to be a few years behind the early research phase, and I think we’ll see in the next couple of years whether NGS makes a leap to the clinical and the diagnostic markets as well.”
Alex said the biggest challenge for big data now is less about the size of the data, which is more a technical challenge that is possible to overcome, but how to train the people to analyse the data and how do you provide them with the tools to let them do that.
“Personnel is a big issue for the industry but at the same time you shouldn’t need to be training a clinician to be a bioinformatician, you should be providing them with the tools so they don’t have to be a bioinformatician,” Alex added.
Speaker presentations and their abstracts are available in this blog, where you can also see photos from the day, download the delegate brochure and listen to the podcast recorded by Clinica.