Both the optical bar code and the color change are detected using a microscope and camera with automated detection software. Weitz says they can produce and process a million drops per second.

Thus far, the team has had little funding to develop the technology. For this reason, they have done only some steps of the process, such as the hybridization reaction described above.

GnuBio is currently securing venture funding, according to cofounder John Boyce, formerly head of business development at Helicos, another Cambridge-based sequencing company. GnuBio researchers aim to deliver a beta version of the technology to two customers later this year. "It won't be able to sequence a human genome, but shorter sequences are still of value," says Weitz. Priced at $45,000, the instrument will be significantly cheaper than others on the market.

Translating the research-stage technology into a commercial product will likely be a major challenge. George Church, a pioneer in sequencing technology at Harvard, who serves on GnuBio's science advisory board, predicts that the biggest hurdles will be integrating the different steps of sequencing, such as sample preparation, and creating good, user-friendly software. Unlike competitor Complete Genomics, which offers sequencing as a service and can therefore rely on experts to do the work, GnuBio plans to sell machines.

Jonathan Rothberg, who cofounded RainDance with Weitz, says the company considered pursuing sequencing when it first started. "But we made a business decision there were other things for us to do," he says.