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News Briefs from the ISMB 2005 Conference Floor

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Ariadne Releases OS Pathway Simulator, Plans to Launch Disease Database

Ariadne Genomics is releasing a free pathway simulation tool through its website under the GPL (available at http://ariadnegenomics.com/technology/simulation.html).

The company presented a poster at ISMB describing the software, which uses ordinary differential equations to analyze time-course concentrations in biological pathways. Ariadne's Azat Badretdinov told BioInform that the company is releasing the software in order to get feedback from the community. Ariadne does not plan to commercialize the software, he said, but the company is considering releasing a module that will act as a "front end" to the simulator.

Separately, during a demonstration of its Medscan text-mining software and ResNet database, Ariadne representatives said the company plans to release a database on pathways related to specific diseases in August or September.


Gene Logic to Add 'Pathway Prioritizer' to Ascenta, GeneExpress

Gene Logic has developed a pathway-analysis algorithm called Pathway Prioritizer that it plans to add to future versions of its GeneExpress and Ascenta platforms.

Described by the company in a poster at ISMB, the software tool uses gene expression data to prioritize known biological pathways from BioCarta and KEGG in relation to a particular biological response. The algorithm determines which pathways are most involved in particular disease states, and is expected to have applications in pharmacogenomics, toxicogenomics, and clinical genomics.

Gene Logic's Kory Johnson told BioInform that the company currently uses the algorithm as part of its custom genomics service, but it plans to release it as part of its software products some time before the end of the year.


Accelrys Demos GCG 11.0, Outlines Bioinformatics Roadmap

Accelrys demonstrated new features in GCG 11.0 at ISMB, which is due out in July, and also provided its bioinformatics product-development roadmap for the next year.

GCG 11.0 will offer a number of new features, including ClustalW, updated versions of the PAUP and MEME algorithms, and new functions called SeqStat, SeqConv, SeqManip, and SeqMerge — a graphical sequence-assembly program. The new release will also enable Blast queries to be redirected to a remote server, and will contain so-called "plus" versions of existing programs with enhanced functionality. GCG 11.0 also removes the previous maximum sequence length limit of 350 kb, and accepts several non-GCG file formats, including BSML, GenBank, EMBL, and Fasta.

Accelrys will also release version 3.0 of its SeqWeb browser in July.

Next March, the company plans to release GCG 11.5, which will contain several new algorithms as well as support for SciTegic's Pipeline Pilot, and SeqWeb 3.5, which will include LDAP enhancements. Next July, Accelrys plans to release GCG 12.0, which will include several genome-comparison tools, and SeqWeb 4.0, which will offer improved graphics.


InforSense Launches KDE for Tiger OS, BioSense Grid

InforSense was demonstrating two new products at its booth at ISMB: its KDE workflow platform running on Apple's "Tiger" Mac OS X version 10.4, as well as its new BioSense Grid framework for creating and publishing bioinformatics applications on the Apple Workgroup cluster.

InforSense BioSense Grid is built on the BioTeam's iNquiry bioinformatics cluster and web portal, and includes KDE's workflow, analytics, and web services architecture.


Invitrogen Develops API to Integrate BioPerl with Vector NTI

Invitrogen is writing an application programming interface to enable its Vector NTI customers to integrate the software with BioPerl.

Invitrogen's Kevin Clancy discussed the API at the Bioinformatics Open Source Conference SIG prior to the main ISMB meeting. Vector NTI users working in a Windows environment can use the API to capture external data and bring it into the Vector NTI environment, he said.

The company also plans to launch a Vector NTI user community later this summer, under which it will provide additional services and tools for customers. An Invitrogen spokesperson said that the firm will provide further details on its plans for the API and the user group in around two months.


PLoS Partnership Expected to Boost ISCB Membership

The International Society for Computational Biology is facing a decline in commercial members, Michael Gribskov, ISCB president, said at the ISCB open meeting last week during ISMB.

Gribskov said that the society's overall membership "fluctuates" from year to year as members sign on for conference discounts. The society has projected 1,761 members for the end of 2005, down from 1,924 last year. Nevertheless, he said, commercial members make up a smaller percentage of the total organization year over year — a trend that he said the organization should try to reverse.

ISCB expects that the recent launch of PLoS Computational Biology, the new journal it is publishing in partnership with the Public Library of Science, will increase its overall membership. PLoS has pledged to sponsor ISCB membership for one author for each paper that it publishes.


NCI Sets Date for Vendor-Oriented caBIG Meeting

The National Cancer Institute will hold a special meeting for vendors interested in participating in the NCI's Cancer Biomedical Informatics Grid project on Sept. 30, according to Peter Covitz, director of bioinformatics core infrastructure at the NCI Center for Bioinformatics.

NCI officials said at the caBIG annual meeting in April that the initiative was planning to host a "vendor-oriented" meeting, but had not set a date for it at the time [BioInform 04-18-05].

Ken Buetow, director of the NCICB and coordinator of caBIG, said at the time that the project wanted to attract participation from commercial vendors, who would be viewed as a "full partner" in building the caBIG architecture.

Covitz told BioInform that the agenda for the meeting is still under discussion, but goals include educating vendors on what it means to be caBIG-compliant, as well as potential advantages of caBIG compliance from a business standpoint.

Talks from several vendors who are currently involved with the project are also planned.


OBF Seeks Members in Bid to Expand Role in OS Community

Looking to play a larger role in the open source development community, the Open Bioinformatics Foundation has passed new bylaws that define the terms of membership in the organization as well as its mechanism for electing new officers.

Founded in 2001, the OBF hosts the annual Bioinformatics Open Source Conference and provides administrative support for BioPerl, BioJava, BioPython, and several other open source bioinformatics projects. "So far, our approach has been to stay low-profile," said Hilmar Lapp of the Novartis Research Foundation, who serves as OBF parliamentarian. However, Lapp said during a talk at BOSC, the founding OBF members recently determined that the organization should pursue "a more ambitious vision."

In line with this decision, the OBF board passed new bylaws to formalize the terms of membership in the organization. "Any individual, business, or organization having an interest in the objectives of the OBF is eligible to apply," Lapp said. There are no membership dues, he added.

The OBF board also elected Jason Stajich, a graduate student in genetics at Duke University, as president to replace founding president Ewan Birney, who resigned [BioInform 06-27-05]. Stajich told BioInform that the organization intends to play a more active role in guiding the open source community by organizing hackathons and other events. Previously, he said, "We hadn't reached a mature decision about what we wanted to do." Now, he said, "We'd like to plan more than one year out."


Who's Hiring?

The ISMB job board was a bit more crowded than it's been in prior years, with a total of 38 organizations posting notices in search of bioinformaticists, computational biologists, or biostatisticians.

The bulk of the postings were in academia and government, and most of the open positions were postdocs, but it appears that interest from industry is picking up a bit. Genentech, Monsanto, Affymetrix, Syngenta, KeyGene, SRA, and GeneGo are all seeking new bioinformatics talent.

 

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