The rapid growth of high-throughput laboratories presents an enormous data management challenge which, reports Russ Swan, is being met by a new breed of software
Perhaps the biggest change in laboratory practices in the last decade or two has been the inexorable rise of high-throughput systems, capable of performing and analysing experiments on an unprecedented scale.
Robots perform the mechanical laboratory tasks in a fraction of the time that a human operator would take, and examine the outcomes to provide a virtual tsunami of data.
The sheer volumes of data being created by a modern high-throughout laboratory create their own problems, chiefly of course in their analysis.
This is where the relatively new discipline of bioinformatics comes into its own, striving to turn this great flood of data into actual useful information.
Large-scale and high-profile initiatives like the Human Genome Project may have caught the public attention, but the human is only one of thousands of organisms which are currently having their genomes deciphered - and consequently the vast data generated by it are merely a drop in a very large ocean.
Much of the early development of bioinformatics software packages is in the relatively exclusive area of customised solutions.
"The industry is unique in that customised solutions are provided to adopters," notes Frost and Sullivan research analyst SM Vinod.
"The customisation process enables end users to choose according to their requirements, allowing the solution to match the needs of the diverse sectors within the life sciences market".
The custom approach is typical of a young discipline, and will doubtless lead to standardised off-the-shelf packages becoming more widely available in the near future.
In this, the bioinformatics market is expected to mimic other specialised laboratory applications, notably the laboratory information management system, or Lims.
In the meantime, the challenges presented by this new technology encourage those in the field to seek out joint ventures and cooperation opportunities.
Danish software house CLC Bio recently announced a new arrangement with the Beijing Genomics Institute and fellow Danes SD Genomics to tackle the problem of computing and understanding the huge volumes of research data created in both academic and commercial research laboratories.
Wang Jian, CEO of the Beijing Genomics Institute, observed that the problems were being faced by practically all researchers all over the world: "They simply don't have the solutions to help analyse and provide understanding of the massive amounts of biological data produced".
"This collaboration brings together a group of companies with the capability and strength to break down these barriers and provide those solutions".
Massively parallel ultra-high-throughput sequencing systems, such as those from by Helicos, ABI, Illumina, and 454, will continue to grow in power and as a result will continue to create larger data volumes.
Wang said the CLC Bio and Beijing Genomics Institute aim to remove barriers by collaborating in the development of innovative plug-ins for use with CLC Bio's workbench platform, as well as implementation of some of BGI's existing genomics tools to be used through CLC Bio's software.
Jens Sundbye, CEO at SD Genomics, added that the collaboration will have widespread implications: "It will not only be an advantage for existing customers like Merck and Novo Nordisk; any global customer - small, medium or large - will have new, intriguing possibilities to get better results in less time, and remove essential barriers in their workflow".
While many feel the need to join forces to tackle this large and complex computational issue, some relatively small firms have been seen to be punching above their weight in the sector.
Notable among these is Biomatters, a New Zealand-based start-up which has won many friends by offering an open-source bioinformatics package called Geneious.
The company says that the release, a couple of months ago, of Geneious Pro 3.0 enables any scientist with a internet connection to organise, access, visualise, and analyse genomic information in a single desktop platform.
This is the fully-fledged commercial version of its package, but unusually the company also offers a powerful free version.
This has proved to be remarkably popular, gaining a top position on the Apple software download chart in 2006.
Company founder Daniel Batten commented that the result was a welcome boost and the 50,000 downloads were about three times the expected number: "We now have users in 70 countries, including big names like Pfizer, Stanford, the American National Institute of Health, Yale, Oxford, and Cambridge".
The free download paved the way for the commercial Geneious offering, at the time of writing version 3.0, which is described as a 'backbone' application connecting the spectrum of biological science.
CEO of Biomatters Candace Toner believes the Geneious platform has the potential to become the unifying platform of the scientific community.
"Geneious can retrieve and categorise scientific information from any data source on the web, allow peers to collaborate in real time, interface with lab equipment and other applications and users can customise their own plug-ins".
"It really is the Holy Grail of science software".
Whether these bold claims will be borne out, only time will tell.
What is clear, however, is that the growing power and utility of bioinformatics software is easing the pressure of the data volumes in high-throughout laboratories.
The bottleneck is becoming less restrictive - but may perhaps be shifting to a new position.
There is a certain irony in the observation that the next constriction point is likely to be, once again, with humans.
The robots have taken over the laboratory, and the microchips have taken over the arithmetic, but these are simply tools which are of limited use without skilled operators.
The industry is becoming aware of a painful shortage of skilled bioinformaticians who can use those tools to maximum effect.
The wheel has turned almost full circle.
