Open source to the rescue of gene analysis

Summary:Scientists can upload data sets directly and the system compares them to known gene sequences. This allows the sample to be quickly categorized.

Genomic Analyzer from 454, a unit of RocheThere is a bottleneck in the genetic revolution.

We're bringing in all sorts of samples but there is not enough genetic sequencing capacity to handle it all.

The science is called metagenomics, the study of microbial genes found in the environment.

Open source is rushing to fill the gap with a server called MG-RAST, for Meta Genome Rapid Annotation using Subsystem Technology.

Scientists can upload data sets directly and the system compares them to known gene sequences. This allows the sample to be quickly categorized.

Now there is a commercial advantage here. The system works only with files generated by the 454 Genome Sequencer FLX System, produced by Roche. Word of this came in a Roche press release.

MedGadget profiled this system in terms of its work in identifying germs found on American soldiers in Iraq a year ago. The picture is from that report.

But the bottleneck is there, even if it's created by a proprietary device, and this open source system is clearing that bottleneck.

The result should be quicker identification of what is out there before it kills you. Which in this case is the bottom line.

Topics: Open Source

About

Dana Blankenhorn has been a business journalist since 1978, and has covered technology since 1982. He launched the Interactive Age Daily, the first daily coverage of the Internet to launch with a magazine, in September 1994.

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