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Biology meets IT... again

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More than bioinformatics, systems biology is the coming thing, even if at first it confused Michael Kenward

The concept of 'systems biology' first grabbed more than passing attention on my part, because I was working on a document for the University of Edinburgh. The university has plans for something it calls the 'informatics hub,' a 50 million expansion plan. In working on the words, I managed to confuse bioinformatics with systems biology. Naturally enough, I went out on to the web to try to find a decent definition and explanation of what systems biology means to its practitioners. By luck, I found an article by Professor Denis Noble in the Nature Encyclopedia of Life Sciences. (They spell in American.) The lucky bit is down to the fact that they had an offer of a month's free access. Otherwise you have to pay, so check to see if there is an institution account somewhere near you. http://www.els.net.

The potted description I arrived at says systems biology 'looks at cells and their function at a "systems" level, building on our understanding of genes, proteins and other molecules to study how they interact. The aim is to build computer models that can tell us something about how the human body works and can throw light on how diseases develop.'

In other words, systems biology will demand a massive conjunction of biology and IT. Naturally enough, there are plenty of websites on the subject. Start at the Institute for Systems Biology http://www.systemsbiology.org/. This tells us that it all began with the human genome project, which 'has catalysed two paradigm changes in contemporary biology and medicine - systems biology and predictive, preventive and personalized medicine'. There's plenty of good background reading on the subject, on what is a nicely designed website.

The institute, based in Seattle, is itself 'an internationally renowned non-profit research institute dedicated to the study and application of systems biology'. The brains behind the place include Leroy Hood, one of the grand panjandrums of gene sequencing. As you would expect of such an operation, there are already several spinout companies from the institute. One such business, Accelerator, seems particularly interesting. Not so much a company in itself, but a life support system for people who want to turn their ideas into products, Accelerator, at http://www.acceleratorcorp.com, promises access to facilities, people, venture capital and management skills. There are also links to more conventional spinout businesses on the web-site of the Institute for Systems Biology. Most of them are common or garden biotechnology businesses. Nothing wrong with that, but not as interesting as businesses that really do break new ground.

One company has at least come up with an imaginative name. Beyond Genomics tells us that it was set up with the mission 'to apply systems biology to discovery and development to create superior treatments for human diseases.' It might be worth visiting this site to see the sort of thing that companies hope to get out of systems biology. http://www.beyondgenomics.com

Systems biology has attracted some of the major research institutions, but they don't seem to be up to speed when it comes to creating web resources. Harvard Medical School set up a new Department of Systems Biology last September, Harvard's first new department in 20 years, but its web presence remains 'under development'. Check the URL from time to time http://sysbio.med.harvard.edu/. Or ask one of those robots to monitor it for you.

(As an aside, an update on one of the web watchers that I have mentioned here before. Copernic Agent used to provide me with this feature as well as intelligent searching. But I now use a standalone program from the same people. Copernic Tracker is much better and offers better configurability http://www.copernic.com. It watches a growing number of websites for me, including, now, the Harvard page.)

MIT was quicker off the mark. There, the MIT Computational and Systems Biology Initiative (CSBi) describes itself as 'a campus-wide education and research program that links biology, computer science and engineering in a multidisciplinary approach to the systematic analysis and computational modelling of complex biological phenomena'. This 'manifesto' underlines the interdisciplinarity of systems biology http://csbi.mit.edu/.

I have mentioned one software weapon that I deployed in researching systems biology; another good tool is the news search feature from the world's favourite search engine. Google News Alert can take a phrase like 'systems biology' and send you a daily message of new stuff it has found http://www.google.com/newsalerts. Messages usually report two or three new links. Alerts tend to focus on companies doing things, rather than universities. (It is surprising how many start-ups describe themselves as 'leaders' in systems biology.) But that may be because companies put more effort, and money, into maintaining web sites.

One company I found in this way is BioSeek, which has some good pointers to articles in the specialist media http://www.bioseekinc.com. One good background feature, with some history, is in the biotech magazine Signals http://www.signalsmag.com/. Just search on the 'systems biology'.

Google's alert can even spot things on familiar sites. For example, it found a page on the European Union's excellent news service, Cordis, about 'proposals for new and emerging science and technology (NEST)', which includes systems biology. Try the usual search, or anything else scientific for that matter, at what has become an invaluable site for keeping track of research that the EU supports http://dbs.cordis.lu/.

Searches can also throw up some strange organisations. What, I wonder, are we to make of something calling itself Betterhumans, at http://www.betterhumans.com? I'll leave you to work that out for yourself .