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mzData, NSF To Award $29M for Phyloinformatics, IBM, Mass General, Teranode, Physiomics


Mass Spec Vendors Vow to Adopt mzData

Several mass spectrometry vendors plan to adopt the mzData exchange format developed by the Protein Standards Initiative, BioInform’s sister publication ProteoMonitor reported last week.

Agilent, Bruker Daltonics, Kratos, ABI, and Waters said they intend to adopt the XML-based format, which standardizes peak lists in a single format.

Many of these companies plan to release products that use the new format by spring 2005, ProteoMonitor reported. Agilent said it will support mzData in its next release of its SpectrumMill analysis software in the late spring or early summer of next year, while Matrix Science said that mzData would be incorporated into Mascot 2.1 beginning next year.

NSF To Award $29M for Phyloinformatics Projects

The National Science Foundation is soliciting proposals for computational phylogenetics and phyloinformatics projects as part of its “Assembling the Tree of Life” initiative, which plans to construct a phylogeny for the 1.7 million described species on Earth.

Last week, NSF issued a program solicitation seeking “projects in data acquisition, analysis, algorithm development and dissemination in computational phylogenetics and phyloinformatics.”

NSF said it plans to award between three and six awards in fiscal year 2005 and again in 2006, with a total of $14 million earmarked for FY 2005 and $15 million for FY 2006. Awards will range up to $3 million each, for durations up to five years.

Proposals for the FY 2005 awards are due March 28, 2005. Additional information is available at

Last October, NSF awarded nearly $20 million to phyloinformatics projects under the same initiative [BoInform 10-06-03].

IBM and Mass General Partner on Cancer Research Grid

IBM said last week that it is working with Massachusetts General Hospital to develop a distributed computing infrastructure that will enable collaboration and information sharing among cancer researchers.

Researchers at IBM’s Cambridge, Mass., research lab have linked several eServer pSeries supercomputers on Harvard’s Crimson Grid and at MIT with multiple IBM eServer Bladecenter servers at the IBM Cambridge facility.

The grid-based system will be used to support brain tumor modeling as part of the NCI-funded Integrative Cancer Biology Program. MGH researchers are integrating genomics, proteomics, and molecular imaging data to model a tumor on multiple scales, from a single cell up to a neoplasm with millions of interacting cells.

IBM said it is also developing a Linux-based, high-resolution video wall with 9.2 million-pixel monitors to provide MGH with the visualization capabilities required for the advanced modeling of tumors.

Teranode Partners with Affy, The MathWorks, and KEGG

Teranode said last week that it is partnering with Affymetrix, The MathWorks, and the KEGG pathway database to extend the capabilities of its Teranode Design Suite modeling platform.

The development partnerships will enable information from KEGG, data generated by the Affymetrix platform, and models created with The MathWorks’ Matlab technical computing software to be translated into VLX (Visual Language of Experimentation), an XML implementation that describes experimental protocols and biological models in the Teranode Design Suite.

The VLX format supports simulated and experimental data, annotations, workflow automation, and audit trails, Teranode said.

The company said it is using the Affymetrix Development Kit to ensure that its software is integrated with Affy’s platform.

In addition, Teranode said it has acquired a KEGG developer license from Pathways Solutions, the Tokyo-based licensor of KEGG data, to support data and model repository development with VLX.

Finally, the partnership with The MathWorks will enable researchers to translate between Matlab programs and VLX, Teranode said.

Physiomics to Use Cell Cycle Modeling Platform in Cronos Collaboration

Physiomics will select drug targets for Cronos Therapeutics using its cell-cycle simulation software, the UK-based companies said last week.

Physiomics, located in Oxford, will use its mammalian cell cycle model, which is linked to PK-Sim drug delivery software from Bayer Technology Services in Germany [BioInform 09-20-04], to select the best targets for Cronos’ GeneICE gene silencing technology.

GeneICE prevents transcription by using cellular gene repressor complexes that interact with the target gene and modify its chromatin structure, Cronos said.

Filed under

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