Skip to main content
Premium Trial:

Request an Annual Quote

Sun, Partners to Launch Industry-Wide OpenPlatformDevelopmentEffort

Premium

Sun Microsystems is partnering with the Biotechnology Industry Organization, the National Cancer Institute, and several commercial bioinformatics vendors to support a massive collaborative effort to develop an open platform for the life sciences based on Java and XML.

The proposed initiative, which has yet to be named, follows fast on the heels of the first meeting of Sun Microsystems’ Informatics Advisory Council held November 29-December 1 in Palo Alto, Calif. In a webcast held February 16, Sia Zadeh, group manager of Sun’s life sciences division, laid out the key findings of the first IAC summit, where delegates from industry, government, and academia discussed issues that impact the life science computing community.

Members of the IAC include representatives from GlaxoSmithKline, Monsanto, the National Research Council of Canada, Oxford Glycosciences, Pedigree Masterfoods, the University College of London, the University of California-San Diego, the University of Chicago, and the University of Minnesota.

Zadeh said that the top IAC request was for an open platform to support data integration and interoperability, closely followed by the need to control the “proliferation of standards” in the field.

The new effort, which is still in the exploratory stage, builds on the findings of the IAC. Zadeh and representatives from several collaborating organizations officially introduced the initiative at the BIO CEO and Investor conference last week in New York, and welcomed the involvement of other members from the pharmaceutical and biotech industries.

Zadeh said that Sun and its industry partners recognized the need to involve as large a portion of the life science community as possible in the development of the platform, “because it makes no sense to create a solution without identifying the problems.”

Jim Lindelien, CEO of Time- Logic, one of Sun’s partners in the platform initiative, added, “We all recognize now that there can’t be one solution from any one vendor.” In addition, TimeLogic, Blackstone, Incogen, LabBook, and Oracle have signed on to participate in the development of the platform and facilitate the development of Java and XML standards.

LabBook has already made the DTD for its BSML XML-based bioinformatics markup language available on its website. Incogen’s CEO Maciek Sasinowski said Incogen would also make the DTD for its XML-based VBML (visual bioinformatics markup language) freely available to support the effort. Sasinowski said that “it makes commercial sense” to support open standards in order to encourage integration in the community.

Lindelien called XML the “grease in the gearbox” that will help users tailor the information they have access to within their own browsers as the industry moves away from the current web portal data-delivery model.

Sun intends to contribute the underlying infrastructure for the open platform, and launched its SunONE (Open Network Environment) initiative earlier this month as a first step in that direction. Zadeh said the infrastructure would allow participating service and application providers to plug their solutions into the platform and ensure interoperability.

Sun and its partners foresee the platform as the eventual hub for a broad variety of life science computing needs, including bioinformatics, cheminformatics, genomics, proteomics, pharmacogenomics, metabolomics, and clinical informatics.

The initiative intends to support the efforts of the Object Management Group’s Life Sciences Task Force, and may work with the OMG to ratify the Java and XML standards the community determines by consensus, Zadeh said. In addition, the initiative fully supports the bioJava and bioXML open source groups and may deposit its open standards in the open-bio.org website. Sun will host a bioXML workshop at the Bioinformatics Open Source Conference that precedes this year’s Intelligent Systems for Molecular Biology Conference in Copenhagen in July.

In addition to its work on the open platform initiative, Zadeh said that Sun’s software systems group has begun to develop improved data visualization hardware and software through its software systems group.

Sun also intends to create several life science integration centers to foster convergence and integration in the industry. Sun is now “looking into various options” for these centers, Zadeh said, which would be similar to clinical systems integration centers that the company has already developed.

The open platform initiative partners will next hold a technical planning meeting on March 3 to define the infrastructure in order to produce a prototype, which will be demonstrated June 24-27 at the BIO 2001 conference in San Diego.

The next IAC meeting will be October 23-24 in Palo Alto.

—BT

Filed under

The Scan

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.

Mitochondrial Replacement Therapy Embryos Appear Largely Normal in Single-Cell 'Omics Analyses

Embryos produced with spindle transfer-based mitochondrial replacement had delayed demethylation, but typical aneuploidy and transcriptome features in a PLOS Biology study.

Cancer Patients Report Quality of Life Benefits for Immune Checkpoint Inhibitors

Immune checkpoint inhibitor immunotherapy was linked in JAMA Network Open to enhanced quality of life compared to other treatment types in cancer patients.

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.