Agilent grants for systems biology software development

RE: Agilent grants for systems biology software development

Dear Kevin,
I am writing to you on behalf of Leo Bonilla, Director of Marketing for Integrated Biology, Agilent Technologies, Inc. Leo and the Integrated Biology team at Agilent have been reading your blog, My Weblog on Bioinformatics, Genome Science, Next Generation Sequencing, and thought you may be interested in sharing a funding opportunity with your readers. Agilent is fostering integrated, whole-systems approaches to biological research through two $75,000 US grants (application deadline August 12, 2011). Funds will support academic or nonprofit research projects covering the development of open source software tools for integrating data from different omics platforms—genomics, transcriptomics, proteomics, and metabolomics. For full details on eligibility, submission, and review process, please visit www.Agilent.com/lifesciences/emerginginsights.
If you have any questions or would like to interview Leo about the grant program, I’d be happy to set up a phone call. Just reply to my email and I’ll connect you with Leo.


Readers if you have any questions post them in the comments and I shall pass them on :)



Fostering integrated, whole-systems approaches to biological research with two $75,000US grants for open source data-integration tool development The different omics platforms—genomics, transcriptomics, proteomics and metabolomics—are generating new insights into how biological systems work at a molecular level. Although each individual omics approach provides a global view of a specific cellular process, this view is limited to only one aspect of the biological system. In order to gain a comprehensive understanding of the system as a whole, researchers are faced with the challenge of merging these very different data sets.
Agilent is supporting scientists who are taking on this challenge through our eMerging Insights Grant Program. We currently have two open initiatives for academic and non-profit researchers developing and/or improving open source, Agilent-compatible software tools to integrate multi-omics data. Each initiative will provide $75,000US to a single academic or non-profit research lab in fiscal year 2011. A proof-of-concept prototype or working solution must be demonstrated at the end of one year, using either existing data sets from the investigator’s own lab or institution, or from new or existing datasets produced at Agilent.
One of the most important outcomes of our eMerging Insights Grant Program is the development of open source* solutions for the analytical life science community. Any tools developed with this funding will be freely available, open source tools for the research community.
The submission deadline for these two initiatives is August 12, 2011.
Awards will be announced September 30, 2011.
*All free or open source licenses are acceptable except "any license requiring , as a condition of use, modification and/or distribution of the software subject to the license, that the software or other software combined and/or distributed with it be (i) disclosed or distributed in source code form; (ii) licensed for the purpose of making derivative works; or (iii) redistributable at no charge. Excluded licenses include, but are not limited to, the GPLv3 License."

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Exome Sequencing hints at sporadic mutations as cause for mental retardation.

1st spotted off Genomeweb
NEW YORK (GenomeWeb News) – De novo mutations that spring up in children but are absent in their parents are likely the culprit in many unexplained cases of mental retardation, according to a Dutch team.
Using exome sequencing in 10 parent-child trios, the researchers found nine non-synonymous mutations in children with mental retardation that were not found in their parents, including half a dozen mutations that appear to be pathogenic. The research, which appeared online yesterday in Nature Genetics, hints at an under-appreciated role for sporadic mutations in mental retardation — and underscores the notion that mental retardation can stem from changes in a wide variety of genes.

 I think it's fascinating to find so many new mutations and changes in DNA that may affect one's quality of life, simply by sequencing the coding regions (and not all of it if I may add). This paper is fascinating as it raises the question if deleterious sporadic mutations are unlikely culprits for a whole variety of diseases that have a genetic risk.
it is certainly more likely that such an event will occur in coding regions but I do not doubt that for some diseases, perhaps the non-coding regions (that play a regulatory role) might have the same effect. If it was a clear cut mutation that results in a dysfunctional protein, and there's no redundancy in the system, it is likely the system will crash. whereas, if it was changes in the expression levels, it might lead to a slightly wobbly system that just doesn't function as well.

While everyone else is waiting for Whole Genome Sequencing to drop in price. There are groups already publishing with exome data. I think in 6 months time, we will see more WGS papers coming up... It's an exciting time for Genomics science!

See the full paper below

A de novo paradigm for mental retardation Nature Genetics | Letter