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BBSRC, DNAStar, Xennex, Japan Patent Office, University of Washington

UK’s BBSRC Awards $12.3M to Support Long-Term Bioinformatics Resources
The UK’s Biotechnology and Biological Sciences Research Council has awarded its first grants under a “pilot” fund to support bioinformatics databases and other resources that are necessary for biological research.
The Bioinformatics and Biological Resources Fund aims to support “high-quality, strategically relevant [resources] that are necessary to underpin the UK's international quality bioscience,” the funding agency said in a statement. The fund is intended to provide “proper support for resources such as databases, genetic resources and culture collections, which require long term maintenance and curation.”
The BBSRC this week announced that it has awarded £6.3 million ($12.3 million) to 10 resources under the initiative. These projects include:
  • Web Services 4 Life Sciences (WS4LS), which aims to provide access to a catalog of web services relevant to the life sciences communities. (PIs: Carole Goble, University of Manchester; Rodrigo Lopez, European Bioinformatics Institute);
  • Wheat Functional Genomics Resource, which will organize the UK’s wheat tools and resources (PI: Keith Edwards, University of Bristol);
  • RevGenUk, or Reverse Genetics in Dicots, a database and reverse genetics platform for the major UK dicotyledonous models (PI: Trevor Wang, John Innes Centre);
  • FlyAtlas, a microarray-based atlas of gene expression in different life stages of Drosophila (PI: Julian Dow, University of Glasgow);
  • Protein Circular Dichroism Data Bank (PCDDB), a database to create, curate, and maintain an electronic archiving and analysis resource for circular dichroism spectroscopy (PIs: Bonnie Wallace, Birkbeck College; Robert Janes, Queen Mary, University of London);
  • CATH – Protein Structure Classification, a hierarchical domain classification database of protein structures in the Protein Databank (PI: Christine Orengo, University College London);
  • InterPro, a documentation resource for protein families, domains, and functional sites, which combines the efforts of a number of databases, including PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D, and PANTHER. (PIs: Rolf Apweiler, EBI; Alex Bateman, Wellcome Trust Sanger Institute);
  • Modeling Portal for UK Plant Systems Biology, which will develop a portal of plant growth models relevant to the systems biology and crop sciences communities (PI: Helen Ougham, University of Wales; Andrew Millar, University of Edinburgh);
  • BioModels, a reference resource for storing, annotating, and sharing quantitative biological models (PI: Nicolas Le Novere, EBI);
  • BioGRID, a resource for accessing comprehensive interaction datasets across multiple model organisms (PI: Mike Tyres, University of Edinburgh).

Oklahoma Foundation Licenses DNAStar's Sequencing Software
DNAStar said this week that the Oklahoma Medical Research Foundation has licensed its Lasergene sequence analysis software.
Under the site license agreement, the medical research non-profit will use Lasergene software in its research into the causes and cures of heart disease, Alzheimer’s disease, cancer, and diabetes.
Financial terms of the agreement were not disclosed.

Xennex Licenses GeneCards Database to JPO, Signs Japanese Distributor
The Japan Patent Office has licensed Xennex’s GeneCards database for use in reviewing patent applications, the Cambridge, Mass.-based company said this week.
In addition, Xennex said that Bioscene Informatics will exclusively distribute GeneCards in Japan.
Under the license agreement, the JPO will use the database to conduct prior art research to determine if an invention can be patented.
GeneCards includes mined genomic, proteomic, and transcriptomics information, and focuses on functional genomics and disease.
The JPO includes the departments of General Affairs, Examination, and Appeals, which together grant patent rights, draft plans for IP policies, manage international exchange and cooperation, conduct IP review, and disseminate IP information.
Financial terms of the agreement were not released.

Baker Lab Launches ‘Foldit’ Protein-Folding Game
Researchers at the University of Washington have added a new twist to the distributed computing model for large-scale computational biology projects with the launch of Foldit, an online game in which players compete to design the “best” proteins.
The game is built on the Rosetta protein prediction software developed by UW’s David Baker, and is an offshoot of the [email protected] distributed computing project that runs the Rosetta software on PC cycles donated by around 200,000 users around the world.
Baker said in a statement that many [email protected] users found that the software could use a little help in its task of testing every possible combination and shape to find the best configuration. “People were writing in, saying, `Hey! The computer is doing silly things! It would be great if we could help guide it,'” Baker said.
Baker began working with a number of colleagues, including by UW computer scientist Zoran Popoviæ, to create a more interactive version of the software that include a competitive angle in order to attract the interest of users.
Foldit trains players on the basics of protein folding through several “practice levels” before allowing them to work on real proteins. “Our main goal was to make sure that anyone could do it, even if they didn't know what biochemistry or protein folding was,” Popoviæ said in a statement.
Currently, the game uses only those proteins whose three-dimensional structures have been solved by researchers, so it is possible to determine the “winner” for any given molecule.
Next, the team plans to introducing proteins with unknown structures. In the fall, they plan to release a version of the software that will allow players to design completely novel proteins from scratch.

Filed under

The Scan

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Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.