EU SIMDAT Consortium Wraps up ‘Virtual’ Drug Discovery Project with GSK
InforSense and its partners in SIMDAT, a European Commission-funded grid technology consortium, have completed a pilot project at GlaxoSmithKline to enable virtual drug discovery through virtual outsourcing of data analysis via secure grid technology, InforSense said this week.
The EC’s Information Society Technologies Programme has been funding the project in the context of SIMDAT, an €11 million ($14.8 million), four-year venture that began in 2004 with a total of 27 partners.
The project partners include NEC Europe, BioFocus DPI, the European Molecular Biology Laboratory, Université Libre de Bruxelles, IT Innovation, and Fraunhofer Institute for Algorithms and Scientific Computing.
The project involved setting up a secure grid-enabled environment to support the electronic outsourcing of data analysis and annotation of biological data to third parties, thus enabling “virtual outsourcing.”
The system, built using InforSense workflows, runs across a test-bed comprising five different remote sites and incorporates data services from two external companies.
“SIMDAT has enabled us to test out all the components we need to support the virtual outsourcing of data analysis in a secure environment,” said Rob Gill, head of biology domain architecture at GSK, in a statement.
Imaging, Software are Focus of Two New NIH Research Centers in California
The National Center for Research Resources has funded two new Biomedical Technology Research Centers, one at the Northern California Institute for Research and Education in San Francisco and the other at the University of California, San Diego, which aim to apply imaging technology to study degenerative diseases, such as Alzheimer’s disease, and software for identifying and analyzing sets of interacting proteins that are important in a wide range of diseases, such as cancer.
These two new centers join 50 other Biomedical Technology Research Centers in the US.
NCIRE will receive a five-year award up to an estimated $6.04 million to develop a center for magnetic resonance imaging of neurodegenerative disorders. Michael Weiner is the principal investigator.
A second award of $4.94 million will fund UCSD’s Pavel Pevzner creation of a center for computational mass spectrometry, in particular developing mathematical approaches and open-access software tools to help researchers work with and analyze proteomics data. The center will also train the scientific community in using technologies that it develops.
NIH to Support Comprehensive E. coli K-12 Data Resource
The National Institutes of Health has committed around $1 million in 2009 funding to support a model organism database for the K-12 strain of the Escherichia coli bacterium.
NIH said in an announcement it will award a single award of approximately $1 million next year and up to $700,000 per year over the subsequent three years for the database, which will serve as a “central resource” for K-12 data.
The funding announcement is a reissue of a similar commitment that NIH announced in 2005 that ultimately supported the development of EcoliHub, a resource that uses web services to integrate various existing K-12 databases. The resource includes a workbench for analyzing K-12 information, software to analyze K-12 structural information, and other features.
The new RFA solicits cooperative agreement applications to develop a resource that will “organize and increase the utility of sequence, sequence annotation, high-throughput data, data-mining algorithms, mathematical models, structural and functional data, and legacy information related to the biology of the K-12 Group, while identifying and filling any gaps in informatics activities needed by the research community.”
The K-12 Resource will provide access to existing sources, as well as internally generated data and information, NIH said, adding that it will be “responsive” to the needs of experimental and computational scientists, and will also serve as a “K-12 centric forum for news and announcements.”
Applicants must address four key areas, including: the content, data, and tools to be provided and integrated; the database and website interface design; how the resource will be managed and integrated and how quality will be assured; and how outreach and end-use community relationships will be conducted.
The database will provide access to definitive sequence and genome annotation data, and will utilize new and existing software tools for analyzing and representing data from the experimental literature. It will offer a search and display interface for users with varying familiarity with the K-12 organisms.
VigeneTech and CapitalBio Sign Protein Analysis Deal
CapitalBio, a Chinese biochip company, and image analysis firm VigeneTech said this week that they are partnering to create integrated hardware-software solutions for protein array analysis.
Initial OEM products will be built around VigeneTech’s MicroVigene microarray image analysis software. The hardware control component would be embedded in the MicroVigene protein array analysis suite, which supports all types of protein array application platforms.
No financial details of the partnership were released.
Biogemma Extends Partnership With BioWisdom
BioWisdom announced that Biogemma has renewed its SRS license for a further three-year term. It did not disclose the financial terms of the deal.
SRS is a bionformatics data integration platform for database search and retrieval.
“SRS offer a robust way to gather sequences and related information, with lot of functions supporting data integrations and querying.” said Olivier Dugas, upstream genomics coordinator at Biogemma, in a statement.
“Web services provided by SRS allowed us to build our modular bioinformatics environment, which we now share in the frame of our collaborations with crops research companies,” he added.
Definiens and Hamamatsu to Integrate Tools for Virtual Microscopy
Computational image analysis firm Definiens and imaging device manufacturer Hamamatsu signed a sales and marketing agreement for the European market, according to a statement.
Hamamatsu and Definiens plan to integrate Definiens image analysis platforms — including Definiens Enterprise Image Intelligence Suite, Definiens XD, and Definiens TissueMap — with Hamamatsu’s NanoZoomer Digital Pathology system, a product suite for virtual microscopy.
No further details were released.
Scottish Vet Institute Selects Syngene's 2D Gel Software
Bio-imaging company Syngene said that Scotland’s Royal (Dick) School of Veterinary Studies is using its 2D protein gel analysis software in its sheep disease research program.
The institution is using the company’s Dymension software to analyze protein extracts from sheep with parasitic gastroenteritis, which is the most commonly diagnosed sheep disease in the UK, Syngene said. The aim is to identify key proteins involved in sheep immunity to the nematode causing the disease and other related parasites.
The studies could increase understanding about how natural immunity to these parasites occurs, and could help in the design of vaccines and therapies to prevent the disease.
Jeremy Brown, a research fellow at the veterinary school, said in a statement that the software has simplified the process of aligning gels and clustering data sets from large groups of animals. Brown said that the school has used the software to analyze 2D gel images to compare the mucosal proteome from 24 different sheep and have detected 951 different spots, “with results across gels being surprisingly consistent.”
Financial terms of the agreement were not released.