NHGRI Backs Data Management for 1000 Genomes Project in 2009-2010
The National Human Genome Research Institute said in a statement it intends to fund two research programs over the next two years supporting researchers who will create methods of handling and analyzing data from the 1000 Genomes Project.
The 1000 Genomes Project, a collaboration between NHGRI, the Beijing Genomics Institute Shenzhen, and the Wellcome Trust Sanger Institute, is focused on sequencing the genomes of between 1,200 and 1,500 people worldwide. That program should produce around 20 terabases of sequence data, according to NHGRI.
NHGRI said this week that it plans to issue a request for applications this fall to fund up to six awards in fiscal 2009 for data processing research. This program will seek applicants who will continue to develop, evaluate, and implement methods for producing data types; monitor and integrate data; and develop tools and processes needed to produce the final dataset for the project.
The work will be conducted under the 1000 Genome’s international collaborative consortium.
Data processing pipelines are being set up to use the sequence data, and these will need to be improved and monitored, and new processing steps will need to be added, NHGRI said. The complete dataset will need to be characterized in several ways, and will need to have several types of global analyses, and tools will be needed that can allow the research community to use the data, according to NHGRI.
The second RFA for analyzing the complete dataset will fund around 10 awards in fiscal year 2010. The researchers may characterize and analyze allele frequency distribution and signals of natural election. The funding will go to develop tools that will be needed to work with data and apply them to other studies, such as genome-wide association studies. This RFA will be released in the fall of 2008 in order to allow applicants sufficient time to “develop meaningful collaborations and responsive projects,” the NHGRI said in a statement.
Neither of these programs will support using the 1000 Genomes data for the analysis of genetics of specific human diseases or other phenotypes.
GeneWorks, Synamatix Partner on Second-Generation Sequencing and Analysis Project
Synamatix of Kuala Lumpur, Malaysia, this week announced a partnership with Adelaide, Australia-based GeneWorks to offer sequencing and bioinformatics research support to customers within Asia and Australia.
GeneWorks will be providing sequencing services and expertise while Synamatix will deliver bioinformatics analysis with its SynaWorks platform, a suite of tools for analyzing data from the Illumina and Roche/454 sequencing instruments.
According to a statement, the partnership’s first project involves de novo sequencing of microbial organisms, but the companies did not disclose the species or other details.
Bayer CropScience Extends Text-Mining Contract with Linguamatics
Linguamatics said this week that Bayer CropScience has renewed its contract to use the I2E semantic knowledge-discovery platform.
Bayer has been using I2E since mid-2007, primarily for the analysis of patents and scientific literature. Linguamatics said that the company will now also use the software to “identify trends and activities in the crop protection business.”
Financial aspects of the agreement were not disclosed.
caBIG Establishes Data Sharing Knowledge Center
The University of Michigan will host the Data Sharing and Intellectual Capital Knowledge Center, the first of five knowledge centers in the Cancer Biomedical Informatics Grid, according to a caBIG announcement this week.
The caBIG Knowledge Centers are part of the Enterprise Support Network, an expansion of support resources for caBIG, launched earlier this year [BioInform 06-27-08].
Each Knowledge Center serves as a hub to help the caBIG community deploy caBIG tools, standards, and infrastructure in a specific domain. The DSIC Knowledge Center hosts a centralized repository of processes, model agreements, and other resources to encourage and facilitate data sharing and to “advance scientific discovery consistent with applicable legal, regulatory, ethical, and contractual requirements,” according to a statement.
Services provided by the DSIC Knowledge Center will include domain expertise, analysis and summary of relevant laws, regulations, policies, and standards, and their potential impact on data sharing, the development of decision support and analytic tools, model documents and best practices, authorship, publication, and dissemination of white papers.
NYSTAR Establishes Supercomputing Consortium
The New York State Foundation for Science, Technology, and Innovation announced a $3 million grant over three years from its Center for Advanced Technology Development Program to establish the High Performance Computation Consortium.
The consortium consists of Rensselaer Polytechnic Institute, Stony Brook University, the University at Buffalo, and the New York State Education and Research Network.
Other institutions working with the consortium include Cornell University, Columbia University, New York University, the University at Rochester, the Rochester Institute of Technology, and the City University of New York.
The idea is to provide practical assistance easing access to supercomputing resources at the institutions and to guide users in the utilization of HPC, NYSTAR said in a statement.