Danish bioinformatics technology developer CLC Bio has released what it considers to be its “first but not the last” MLST workbench software for the high-performance computing arena, a technology that has applications in molecular diagnostics.
MLST – for multilocus sequence typing – is a way of tracking workflow for bacteria and yeast isolates, a process that normally takes up to 25 minutes, according to Denmark-based CLC Bio’s users’ studies.
The software enables researchers to “type pathogens faster and much more accurately,” said Roald Forsberg, a senior scientific officer for the company. “We are sort of moving into an age where people can do biological tracking of pathogens of the microorganisms … [such as] tracking the roots of infection throughout, say, a hospital or a community, and I also think these techniques will pop up in bioterrorism.”
Forsberg told BioInform that “this is our first venture into [molecular] diagnostics … We spent the first couple of years, [maybe] a year and a half just building a good platform for our bioinformatics workbenches.”
CLC Bio’s vice president, Jan Lomholdt claimed MLST module users can reap results in about a minute, while easily inspecting and editing sequencing data. “A lot of steps have been boiled down into a couple clicks with the mouse,” he told BioInform.
The new software, which will see its formal debut at next week’s ISMB conference in Vienna, is based on DNA sequence data from myriad “housekeeping” genes. For each gene, data is contrasted to a database full of known alleles.
Forsberg said that at the moment in the biology industry as a whole, “a lot of this typing is done on agrose gels. … People use these gel-based methods; they are all fast methods, good for high-throughput, but they only give you a little bit of information and … they don’t allow for much tracing of the roots of infection because they only allow [one] to distinguish the microorganisms at a very high level, maybe at the species level, but the new DNA-based technology [means that one] is getting a lot more high resolution in one’s work.”
Lomholdt added that “you can say this is a new entry for us because we are going into the molecular diagnostic area, so based on top of our workbench, which [offers] traditional sequencing analysis – and of course that’s always moving – every time we release a new version you see new functionality. The latest [version’s functionality] is RnA, and we use that functionality in [tandem with] our Workbench.”
He added that the solution is architected in a way in which a module is placed on top of a workbench similar to Lego blocks.
“[With our solution] users can type these pathogens faster and much more accurately … We are sort of moving into an age where people can do biological tracking of pathogens of the microorganisms … [such as] tracking the roots of infection throughout, say, a hospital or a community, and I also think these techniques will pop up in bioterrorism.”
Another interesting point is that the software touts the algorithm HMMer, which will purportedly run on an Intel chip system. This detail will also be discussed at next week’s conference.
Intel has a strong working relationship with CLC Bio. “We are working closely with Intel on a roadmap for new high-performance computing,” Lomholdt said.
CLC Bio plans to funnel money it’s received from some fairly deep pockets – according to Lomholdt, VCs with a capital worth of $200 million – into areas that support the development of new algorithms “moving up to the enterprise level.”
Through the funding – the amount of which Lomholdt would not disclose, only saying that it was significant – CLC Bio has been able to launch collaborations that have helped it grow from a small shop to a company with more than 40 staffers, and growing. This week alone, a handful of developers were added to its Danish headquarters.
CLC Bio has also recently announced a collaboration with the Beijing Genomics Institute and SD Genomics to compute and better understand and dissect data culled from academia, biotech, and pharmaceutical companies. CLC Bio and Beijing Genomics are using plug-ins to bridge the solutions for use with CLC Bio’s Workbench platform.
According to a company missive, the volume of data created by new sequencing technologies — among them tools made by Applied Biosystems, Helicos, 454, and Illumina — demands that a “massively parallel ultra-high-throughput sequencing system” be built.