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PlasmoDB, Platform Computing, University of Buffalo, Cancer Research Center, Nonlinear Dynamics


PlasmoDB Coming to a Journal Near You

Last week’s big genomics news: the simultaneous publication of the Plasmodium falciparum parasite responsible for malaria in Nature as well as the Anopheles gambiae mosquito genome that often serves as a carrier for malaria in Science, was not without its bioinformatics component.

The PlasmoDB database ( housed at the University of Pennsylvania released its most recent upgrade, version 4.0, concurrent with the publication of the parasite genome sequence.

In addition, the Penn researchers said they plan to distribute the database to scientists worldwide via a CD-ROM included in the October 31 issue of Nature.

David Roos, director of Penn’s Genomics Institute, who heads the Plasmodium database project, and his co-authors wrote in Nature that “Having the data literally ‘in hand’ provides scientists everywhere with a sense of ownership and involvement in the Plasmodium genome project, expediting the pace of research and discovery.”


Platform Teams with ADA and Entelos on Diabetes Project

Platform Computing said last week that it is partnering with the American Diabetes Association and Entelos to support the high-performance computing needs of the Diabetes Research Forum, a scientific collaboration to advance research for the prevention, treatment, and cure of type 2 diabetes.

Under the terms of the partnership, Platform’s LSF workload management software will run on the Diabetes BioCluster, 24 four-processor AlphaSystem ES40 systems donated by Hewlett-Packard.

The Diabetes BioCluster runs Entelos’ Diabetes PhysioLab software. Platform LSF will “dramatically increase the speed and efficiency of compute-intensive in silico research and development” for the project, according to a company statement.

Research conducted by the Diabetes Research Forum will be provided to pharmaceutical and biotechnology companies participating in the project. Johnson & Johnson Pharmaceutical Research and Development signed on to become the first member of the forum earlier this year [BioInform 06-24-02].


UB Wins NSF Grant to Shake Up Shake-n-Bake

The University of Buffalo has been awarded a $2 million National Science Foundation Information Technology Research grant to support research in new computational approaches to protein structure prediction. Grid computing, data mining, and collaborative environments have been highlighted as focus areas for the project.

The funding will support UB researchers developing methods to enhance SnB (Shake-n-Bake), a protein-structure determination software package developed by scientists at UB and Hauptman-Woodward Medical Research Institute in Buffalo and first released in 1995.

“SnB has had an enormous impact on the crystallographic community,” said Russ Miller, director of UB’s Center for Computational Research, in a statement. “But its ultimate potential is unknown. This grant will allow us to make advances in structure determination by exploiting new computational paradigms.”

Plans include a grid-enabled version of SnB, as well as new agent-based data mining techniques to identify patterns in an SnB data warehouse at CCR.

“Once the data are in the repository, the software agent will continually mine them in an effort to determine adjustments in parameter settings,” said Miller, “so the next time someone uses the package to solve a structure with characteristics similar to those in the warehouse, SnB will be even more efficient.”

Eventually, the UB and HWI developers plan a “virtual community” for protein scientists to collaborate on projects and share their data.


Multi-Center Prostate Cancer Project Now Underway

Fred Hutchinson Cancer Research Center has been awarded $12.7 million from the National Cancer Institute to lead a multi-center, five-year investigation into the genetic mechanisms of prostate-cancer progression.

The initiative, called the Pacific Northwest Prostate Cancer Research Specialized Program of Research Excellence, will involve more than 50 investigators from Fred Hutchinson, the University of Washington, the Institute for Systems Biology, the University of British Columbia, and the Prostate Center at Vancouver General Hospital.

The consortium was awarded $10.5 million from the NIH in July for similar research.

Among four primary research projects planned, Lee Hood of the ISB and Peter Nelson of Fred Hutchinson will lead a team that will analyze gene and protein expression in a range of prostate tumors in order to decipher the molecular pathways that allow disease progression.

A SPORE-funded informatics and gene expression core led by Nelson and Nigel Clegg of Fred Hutchinson will provide gene chip technology and data analysis tools for the large-scale gene-expression studies.

A biostatistical core led by Ruth Etzioni at Fred Hutchinson will ensure that investigators design their studies so that data collection and analysis will yield statistically valid and interpretable results.


Nonlinear Inks Distribution Deal with Amersham

Nonlinear Dynamics of Newcastle upon Tyne, UK, said last week that it had signed an exclusive software product development and distribution agreement with Amersham Biosciences for ImageQuant TL software.

Nonlinear is developing ImageQuant TL as a continuation of the existing ImageQuant software. The new software will be exclusively distributed with all Amersham Biosciences imaging instruments.

Amersham already distributes Nonlinear’s Progenesis 2D gel analysis software.


Filed under

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.