When he first became director of the Scottish Bioinformatics Forum (SBF), Chris Janssen knew he was about to enter terra incognita. Four years later, he realises this will always be part of the job. The SBF will always be discovering new challenges, acting as a bridge between different research pools in Scotland to translate their specialist knowledge and skills into something of value to business as well as the general public – in an area of science where mind-boggling breakthroughs are made all the t…
Article by Peter Barr
When he first became director of the Scottish Bioinformatics Forum (SBF), Chris Janssen knew he was about to enter terra incognita. Four years later, he realises this will always be part of the job. The SBF will always be discovering new challenges, acting as a bridge between different research pools in Scotland to translate their specialist knowledge and skills into something of value to business as well as the general public – in an area of science where mind-boggling breakthroughs are made all the time...
Advances in biology and bioinformatics are happening so fast it's hard to keep up with the news – even for leading researchers. Ten years ago, the SBF director Chris Janssen was doing collaborative research at the Sanger Institute in Cambridge, struggling to sequence a fragment of the malarial genome – a job which, in totality, would have taken several years to complete using the technology available then. Today, it's possible to sequence the whole of the malarial genome five times in only three days. Janssen says that ten years from now it may be routine for individuals to have their genomes sequenced as part of their everyday healthcare. And it is against this ever-changing and increasingly dynamic background that the SBF works, helping with training as well as providing a forum and “matchmaking” leading researchers from universities all over Scotland and further afield.
Janssen says the key role of the SBF is to facilitate “interdisciplinary integration and inter-institutional collaboration,” taking full advantage of the independence it enjoys as a project of the RSE Scotland Foundation, largely funded by the Scottish Funding Council. In practical terms, this means organising a programme of workshops, including in-depth training in the latest techniques and technology, as well as forums to discuss important future trends in bioinformatics – attracting over 2,000 people from academia and industry to recent events. It also organises scientific seminars and conferences, providing a stage for scientists based in Scotland and around the world, focusing on topical issues in computational biology and its impact on modern biomedical and life sciences. In 2010, for example, the SBF organised the International Conference on Computational Methods in Systems Biology, which attracted over 1,200 delegates from 51 countries.
According to Janssen, there has been a revolution in biology in recent years, using new computational methods and hardware to cope with the new kind of data produced – more complex and in much higher volumes than ever before. And this not only leads to breakthroughs in research but means that scientists who graduated several years ago need continuous training to learn the new skillsets required. The SBF is active in providing this technical training, but Janssen also sees its role as helping universities deliver the courses themselves.
The focus groups established by the SBF are also very high on the agenda, including the Scottish Biomodelling Network, which brings together engineers, physicists, informatics specialists and life scientists to discuss the latest developments, identify new challenges and make joint applications for funding. “Sometimes,” says Janssen, “life scientists have major problems to solve but don't have all the tools they need, and sometimes informaticians have lots of powerful tools but don't know what to do with them – and that is why we try to bring the different groups together. In the current financial climate, the importance of this coordination takes on additional significance, since we now have to take every opportunity to share pooled resources.”
Another major project where the SBF is providing support is strategic thinking for IT and informatics capabilities for a national, as well as regional, biorepositories, finding ways to tie together medical records, pathology records and molecular data from all across Scotland to help with the discovery of biomarkers (e.g. for cancer) through data mining – to make sense of the vast amount of data by developing new systems and approaches. This project has now received major impetus from the creation of the Scottish Academic Health Sciences Collaboration (SAHSC) by the Chief Scientist’s Office, NHS Scotland and the universities of Aberdeen, Dundee, Edinburgh and Glasgow. The SAHSC mission is to establish “a world-leading clinical research platform for patient-oriented research,” focusing on key areas such as scanning capabilities, tissue banking, clinical research support and information technology.
The first job, says Janssen, was to sort out the ethical and governance issues by providing “safe havens” for medical records, then move on to the technical issues. And Janssen believes Scotland has several advantages for such a project, including a rich set of data across a broad spectrum of diseases and “excellent international researchers to translate the data into meaningful research results.”
Together with the Edinburgh “GenePool” the SBF has also set up a focus group to discuss important issues in next-generation genome sequencing, looking at new technologies and computational methods dealing with high-throughput gene sequence data. Janssen is convinced that these technologies will be used in medical diagnostics and clinical research within a few years.
In Janssen’s view, life scientists have to “think out of the box” and tap resources that they may not have tapped in the past. And while researchers based in Scotland work in this “rarified sphere” with their finite resources, the SBF tries to have a synergistic effect, not only “closing the loop” between different research pools such as SICSA (the Scottish Informatics and Computer Science Alliance) and SULSA (Scottish Universities Life Sciences Alliance) but also between different disciplines – what Janssen describes as “translating” ideas from one group of researchers to another. “We aim to join up different researchers in a co-ordinated manner that leads to directed interactions,” says Janssen, “introducing novel methods and technologies from one field to another.”
Above all, says Janssen, the SBF is independent and is well placed to provide an “holistic overview” of what is going on in bioinformatics in Scotland, performing a role that individual institutions could never perform on their own. “Only by sharing their expertise and experience will scientists be able to find manageable solutions,” says Janssen, “and translate their bright ideas into concrete action, to compete with other international researchers.” It is all about knowledge exchange, he adds, and the organisation's success can be measured in various ways, including competitive funding, intellectual property, commercialisation, interaction with industry and high-quality publications – as well as “breaking paradigms in research.”