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Genstruct, MDGrape 3, Environmental Bioinformatics Research Center, ISCB, Chinese Academy of Sciences, UC Davis, MAGE-ML Jamboree

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Genstruct Extends Pfizer Collaboration

Genstruct said last week that it has extended a collaboration with Pfizer that began in January 2003.

The new arrangement includes research projects using Genstruct’s Molecular Epistemics platform with a number of Pfizer units including Worldwide Safety Sciences, the Proteomics Global Center of Excellence, and Clinical Sciences.

Specific terms of the multi-year deal were not disclosed.


Riken Demos 32-Tflop Protein Modeling System at Supercomputing 2004

At the Supercomputing 2004 conference in Pittsburgh last week, Japan’s Riken showcased its MDGrape 3 molecular dynamics simulation system on a 16-processor SGI Altix 350 system.

The MDGrape 3 system includes a host computer along with special-purpose chips that calculate electrostatic and intermolecular forces. Riken used the Altix 350 as the host computer and eight specialized MDGrape 3 chips in the demo, which achieved 32 Tflops in a single rack.

Riken plans to build an MDGrape system capable of generating a petaflop by 2006 using 32 racks with 512 Itanium 2 processors and 6,144 MDGrape chips.


EPA Awards $2.25M in Comp Tox Grants, with Plans for $5M More

The Environmental Protection Agency’s newly established computational toxicology program [BioInform 01-12-04] has awarded $2.25 million for three grants, and is soliciting proposals for $5 million in awards to establish an Environmental Bioinformatics Research Center.

The grants were awarded to groups using computational methods to identify hazards and assess risks from endocrine-disrupting chemicals. Michigan State University received two of the grants: $750,000 for a project using a fish model to study chemically induced changes in gene expression patterns; and $748,000 for a project to develop a computational model that integrates rat gene expression data. The University of Florida, Gainesville, received $746,000 to develop a computational model of the flathead minnow response to endocrine disruptors.

In addition, EPA said it is accepting applications for an Environmental Bioinformatics Research Center that will develop “innovative computational methods” to analyze molecular biology data.

The deadline for submitting proposals is Feb. 24, 2005. Further information is available at http://es.epa.gov/ncer/rfa/2004/2004_comp_tox.html.


ISCB Seeks Award Nominations

The International Society for Computational Biology is seeking nominations for two awards: the third annual Senior Scientist Accomplishment Award, which recognizes senior members of the computational biology community, and the fifth annual Overton Prize, which is awarded to scientists in the early- to mid-phase of their careers.

Previous winners of the Overton Prize include Chris Burge, David Baker, Jim Kent, and Uri Alon, while Senior Scientist recipients include David Sankoff and David Lipman.

Recipients of both awards will be invited to present keynote talks at the Intelligent Systems for Molecular Biology conference in Detroit, Mich., June 25-29, 2005.

Nomination forms are available at http://www.iscb.org/iscb_awards_nomin/nomin_form.php, and should be submitted by Dec. 5.


Max Planck, Chinese Academy of Sciences Partner on Comp Bio Center

Germany’s Max Planck Society and the Chinese Academy of Sciences have signed an agreement to build a joint research institute for computational biology.

The MPG/CAS Partner Institute for Computational Biology will be housed on the campus of the Shanghai Institutes of Biological Sciences of the Chinese Academy of Sciences. CAS will provide €5 million ($6.5 million) in funding, and Max Planck €2.5 million.


Sun Taps UC Davis as Informatics COE

Sun Microsystems has chosen UC Davis as a Center of Excellence in Public Health and Safety Informatics.

Sun said it will install around $1 million worth of computer equipment at the center, including 57 Sun Fire V20z servers, one Sun Fire V210 server, and a number of Sun StorEdge 3310 arrays.

The COE will connect UC Davis’s Center for Information Technology Research in the Interest of Society, the Institute for Data Analysis and Visualization, the bioinformatics group of the UC Davis Genome Center, and the Computational Science and Engineering Center.


Stanford to Host MAGE-ML Jamboree

The Stanford Microarray Database group said last week that it will host the next MAGE-ML programming jamboree at Stanford March 21-24, 2005.

There is no charge for attendance, but space is limited.

Registration information is available at http://genome-www5.stanford.edu/mged/.

Filed under

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.