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Java, Software Standards Hot Topics at Recent Sun Summit

NEW YORK, Jan 3 - Java could be a killer app for visually modeling genomic data, but several important problems have to be addressed first, according to Shankar Subramaniam of University of California, San Diego.

Java “is not used very widely” by bioinformatics researchers, said Subramaniam. “There are not enough Java experts in the bioinformatics community, not all the Web browsers are compatible, and it has multiple flavors and varieties. As far as object manipulation and orientation, there need to be standards that are fairly good across multiple operating systems.”

The need for a jump-start to Java is one of the things that Subramaniam and others discussed at the first Informatics Advisory Council Summit held by Sun Microsystems at the end of November. The summit’s purpose was to assess the information needs of the life sciences community and what its place is in addressing these needs.

Sun is planning to issue a report on this summit at the end of February, along with specific announcements on how it will address the life sciences community, said Loralyn Mears, a Sun spokesperson.

Other important issues that experts discussed at the summit included: How the company can get involved with databases, how it can help establish standards for software such as bioperl and bioxml, and how it can participate in high-end computing for sequence-based analysis, Subramaniam said.

On the issue of databases, the participants discussed how Sun and Oracle have to coordinate protocols.

Finally, the participants addressed Sun’s role in helping the OMG (object management group) define computing ontologies, Subramaniam said.

When the report on this summit is issued in February, Mears said, the company expects to announce collaborators on the projects discussed in the meeting.

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