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Pac Bio Launches Developer Network for Upcoming Single-Molecule Sequencer


Pacific Biosciences this week launched PacBio DevNet, an online network intended to support third-party development of informatics tools and standards for the company's Single Molecule Real Time sequencing technology platform.

The company said in a statement that as part of the development of the SMRT technology, it has been working "closely with members of the informatics community to develop and define standards for working with single molecule sequence data," but it decided to launch a more "formal" developer program as it nears the commercial launch of its PacBio RS platform, slated for later this year.

PacBio DevNet is intended to "support the ecosystem of academic informatics developers, life scientists, and independent software vendors" interested in creating tools to work with the company’s sequencing data, the company said in a statement.

The site provides access to data sets, source code, application programming interfaces, conversion tools, and documentation related to SMRT sequencing.

Currently, the site offers web service APIs for instrument control and secondary analysis; algorithms for its resequencing pipeline — a three-step process that includes filtering to remove sequences from empty zero-mode waveguides, mapping of reads against the reference sequence via the company's ReadMatcher algorithm, and a consensus step to determine accuracy and identify variants; and tools for converting PacBio HDF5 files to the FASTA, SAM/BAM, BED, and VCF formats.

The site also includes a section called Code Share that is intended to serve as a directory of open source projects that support the SMRT technology.

Eric Schadt, chief scientific officer for Pacific Biosciences, said in a statement that the company's technology "introduces entirely new dimensions to data, such as a time component, that are unlike anything the bioinformatics community has encountered to this point."

As a result, he said that the company is "committed to supporting third-party software development and facilitating the rapid adoption of this new data type into the scientific community.”

Earlier this year, PacBio launched a commercial partner program intended to help customers "rapidly and easily" integrate its sequencers into existing research infrastructures. The program included six informatics firms among its 11 initial members, including Amazon Web Services, BioTeam, CLC Bio, GenoLogics, GenomeQuest, and Geospiza (BI 2/19/2010).

Other partners included sample-preparation partners Agilent Technologies, Fluidigm, RainDance Technologies, Caliper Life Sciences, and NuGen Technologies.

PacBio said the partners will receive access to information and development tools, application programming interfaces, and protocols. In some cases, the program might lead to co-marketing opportunities or co-development agreements, the firm said at the time.

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