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Funding Update: NSF Bioinformatics Grants Awarded Sept 10 — Oct 22, 2013

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Development of a Novel Computing Instrument for Big Data in Genomics
Start Date: Sept. 15, 2013
Expires: Aug. 31, 2017
Awarded Amount to Date: $1,800,000
Principal Investigators: Steve Lumetta, Ravishankar Iyer,
Gene Robinson, Saurabh Sinha, Cornelis Jongeneel
Sponsor: University of Illinois, Urbana-Champaign

According to the abstract, the funds will support the development of CompGen, an infrastructure that will provide a "vehicle" for biologists and computer scientists to collaborate and develop new algorithms for genomic data analysis and visualization as well as a framework for "developing accelerators and mapping to heterogeneous computational resources and hierarchical database storage." The investigators' development efforts will focus, among other things, on reducing data volume, and optimizing storage hierarchy.


Parallel Algorithms and Software for High-throughput Sequence Assembly
Start Date: Aug. 12, 2013
Expires: April 30, 2015
Awarded Amount to Date: $487,681
Principal Investigator: Srinivas Aluru
Sponsor: Georgia Tech Research Corporation

The funds will support the development of algorithms and a software framework for genome and transcriptome assemblies. Specifically, these tools will target applications such as improved hybrid assembly of sequences from multiple next generation sequencing platforms.


Towards a Self-organizing Map and Hyper-dimensional Information Network for the Human Genome
Start Date: Sept. 15, 2013
Expires: Aug. 31, 2015
Awarded Amount to Date: $250,000
Principal Investigator: Kimmen Sjolander
Sponsor: University of California, Berkeley

According to the abstract, the funds will support the development of a open source computational infrastructure that "models the inherent structure of biological data, by creating a graphical database of genome and proteome data for the human genome and related eukaryotic genomes to model relationships … that cannot be represented effectively in relational databases."


The Arabidopsis Information Portal
Start Date: Sept. 15, 2013
Expires: Aug. 31, 2018
Awarded Amount to Date: $2,434,910
Principal Investigators: Christopher Town, Gos Micklem,
Matthew Vaughn, Konstantinos Krampis
Sponsor: J Craig Venter Institute

These funds will be used to develop the Arabidopsis Information Portal, a new resource that is intended to bring together Arabidopsis data into a single, user-friendly location (BI 9/20/2013).


Advancing the Molecular Epidemiology of Infectious Diseases through Bayesian Phylogenetics
Start Date: Sept. 15, 2013
Expires: Aug. 31, 2017
Awarded Amount to Date: $758,320
Principal Investigators: Marc Suchard
Sponsor: University of California, Los Angeles

According to the abstract, these funds will support the "design, development and distribution of Bayesian statistical algorithms and software for analysis of massive amounts of sequence and phenotype data to study the emergence and spread of rapidly evolving pathogens."


Software Infrastructure for Revealing Gene and Genome Evolution, Anchored by Enhancement of Multiple Genome Alignment Software MCSCAN
Start Date: Feb. 1, 2014
Expires: Jan. 31, 2017
Awarded Amount to Date: $493,692
Principal Investigators: Xiyin Wang, Andrew Paterson
Sponsor: University of Georgia Research Foundation

These funds will be used to enhance the MCSCAN software so that it can help researchers better "reconstruct the evolutionary trajectories of genomes and gene families, including the singularly challenging genomes of angiosperms and other taxa that have experienced polyploidization events."


Methods for Preprocessing Population Sequence Data
Start Date: Sept. 1, 2013
Expires: Aug. 31, 2017
Awarded Amount to Date: $40,000
Principal Investigators: Eleazer Eskin
Sponsor: University of California, Los Angeles

This grant will be used to develop computational methods for analyzing sequence data across populations. Specifically, the investigators will develop methods of compressing sequence data and searching "regions identical by descent across multiple samples, and for high-resolution haplotype inference from sequence data."


PathBubbles for Dynamic Visualization and Integration of Biological Information
Start Date: July 1, 2013
Expires: June 30, 2015
Awarded Amount to Date: $218,690
Principal Investigators: Fiona McCarthy
Sponsor: University of Arizona

This grant will be used to develop PathBubbles, an interactive pathway visualization tool that uses existing Vis- and Code Bubbles as a framework.


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