Bioinformatics

Bioinformatics is playing an increasingly important role in drug development and our understanding of complex genetic and molecular information. Simon Smith, Head of Bioinformatics, J&J talks to NGP about growth and potential breakthroughs.

NGP. In which area of your work would you say there has been the most progress in the last five years, and in which do you predict the next major breakthrough?
The glimmer of an understanding of pathways, and the potential to turn this into a truly useful tool. Most of the early ‘rush’ into genomics, while generating much excitement has not, in itself, led to improved understanding, rather it has raised more questions. Microarrays have entered the mainstream, and although much work has been done again, the true usefulness has not yet been realised.

NGP. Significant progress is being made to map human genetic variations and how all the tens of thousands of genes and proteins work together. Apart from sheer scale, what are the other major challenges in completing this task and narrowing down treatments?
Connecting the dots. The work so far has revealed many surprises and also revealed unexpected complexities. While the ‘low hanging fruit’ appears easier to exploit, truly turning the awakening knowledge of genetic variation into treatment, is proving a daunting task. Not the least because of the social conscious issues it raises.

NGP. How is IT addressing some of those challenges? Is it helping to advance drug development research or make the whole process more time and cost-efficient?
IT and research are often disconnected at present. Vocabulary and understanding of the problems often thwart IT. In several organisations there is now a convergence of IT and basic research- this is a very positive move.

Developing strategies and, more importantly, actual tools which aid communication amongst scientists is starting to make a difference. Use of the web and emerging software platforms like AJAX are at last promising a more flexible and yet more complex approach to be taken.

NGP. What would you say are the core tools of the bioinformatics researcher?
Core tools for bioinformatics are at a crossroads. The earlier days of many companies involved in bioinformatics platforms has eroded, particularly those with costly IP components. In part due to their own success – many pharmas are now suffering from a surfeit of novel targets. Given the sheer magnitude of taking one compound to market as a drug, it is reasonable to see why much of the bold, initial purchases of bioinformatics tools, particularly those with associated IP content has dwindled.

Those that provide pathway information, allow frameworks to be built in a non-proprietary way are proving to have more staying power.

NGP. For bioinformatics to realise its full potential, it requires a merging of skills and information from both medical science side and IT. Would you agree with this and what barriers still exist to making this possible?
I completely agree with this statement. Barriers abound – vocabulary is an obvious one. United in desire, but separated in our own vocabularies and lack of cross fertilisation of detailed knowledge, make this merging, although sorely needed, hard to achieve.

Use of tools, although at first, slightly surprising, is another barrier. Take the more traditional bioinformatics role – often a person with excellent research skills, strong in perl, mysql and apache and other open license software and mix them with IT, often held to different and more corporate software standards and you instantly have a clash.

NGP. What skills do both biologists and computer scientists bring to the bioinformatics table?
A blending of views and of thoughts – broad skills, but essential to good cooperation.

NGP. Looking forward, what do you hope to achieve in the next 5 years? What are the principle areas of focus for your work?
We are focusing on the broad task of supplying completely integrated information with respect to any gene of interest, across many different databases and the stages of drug discovery. To provide a view, not only of information, but knowledge of what is happening and has happened with this gene within our drug discovery sectors. The goal is still, to de-mystify and to simplify, but to preserve easy access to often complex data.