
NSF Org: |
CCF Division of Computing and Communication Foundations |
Recipient: |
|
Initial Amendment Date: | January 28, 2015 |
Latest Amendment Date: | January 25, 2016 |
Award Number: | 1464268 |
Award Instrument: | Standard Grant |
Program Manager: |
Almadena Chtchelkanova
achtchel@nsf.gov (703)292-7498 CCF Division of Computing and Communication Foundations CSE Directorate for Computer and Information Science and Engineering |
Start Date: | February 1, 2015 |
End Date: | November 30, 2018 (Estimated) |
Total Intended Award Amount: | $171,341.00 |
Total Awarded Amount to Date: | $187,341.00 |
Funds Obligated to Date: |
FY 2016 = $8,292.00 |
History of Investigator: |
|
Recipient Sponsored Research Office: |
1903 W MICHIGAN AVE KALAMAZOO MI US 49008-5200 (269)387-8298 |
Sponsor Congressional District: |
|
Primary Place of Performance: |
4601 Campus Drive Kalamazoo MI US 49008-5314 |
Primary Place of
Performance Congressional District: |
|
Unique Entity Identifier (UEI): |
|
Parent UEI: |
|
NSF Program(s): | Software & Hardware Foundation |
Primary Program Source: |
01001617DB NSF RESEARCH & RELATED ACTIVIT |
Program Reference Code(s): |
|
Program Element Code(s): |
|
Award Agency Code: | 4900 |
Fund Agency Code: | 4900 |
Assistance Listing Number(s): | 47.070 |
ABSTRACT
Sequencing of genomes for numerous species including humans has become increasingly affordable due to next generation high-throughput genome sequencing (NGS) technologies. This opens up perspectives for diagnosis and treatment of genetic diseases and is increasingly effective in conducting system biology studies. However, there remain many computational challenges that need to be addressed before these technologies find their way into every day health and human care. One such daunting challenge is the volume of sequencing data which can reach peta-byte level for comprehensive system-biology studies.
Genomic data compression is needed to reduce the storage size, to increase the speed and reduce the cost of I/O bandwidth required for transmission of such data. However, existing genomic compression solutions yield poor performance for Big Genomic Data. Further, the existing state of the art tools require the user to decompress the data before it can be used for further analysis. This project is focused on compression of genomic information and developing a framework which will allow analysis of compressed form of the data. The project develops HPC solutions for fast compression of Big NGS Data sets using ubiquitous architectures such as GPUs and multicore processors. HPC techniques are utilized to compute essential functions such as alignment and mapping using the compressed form of the NGS data. More efficient encoding of the NGS data for better network utilization is also being investigated.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
Note:
When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external
site maintained by the publisher. Some full text articles may not yet be available without a
charge during the embargo (administrative interval).
Some links on this page may take you to non-federal websites. Their policies may differ from
this site.
Please report errors in award information by writing to: awardsearch@nsf.gov.