Peter H. McCartney
DBI Division of Biological Infrastructure
BIO Directorate for Biological Sciences
Start Date:
April 1, 2007
Expires:
March 31, 2010 (Estimated)
Awarded Amount to Date:
$436701
Investigator(s):
Donald Gilbert gilbertd@indiana.edu (Principal Investigator)
Sponsor:
Indiana University
P O Box 1847
Bloomington, IN 47402 812/855-0516
NSF Program(s):
ADVANCES IN BIO INFORMATICS
Field Application(s):
Program Reference Code(s):
BIOT, 9184, 1165
Program Element Code(s):
1165
ABSTRACT
Indiana University is awarded a grant to develop integrated, shared database tools, such as those built under the umbrella of the collaborative Generic Model Organism Database (GMOD) project. Software tools to fully assembly, analyze and compare these genomes are available, but the ability to employ them is limited to those with extensive computational resources and engineering talent. In this project, methods are being developed for use by existing and emerging model organism databases that will address genome database access needs and middleware for comparative analyses. Effective use of shared cyberinfrastructure, such as NSF-sponsored TeraGrid and other Grid systems, is addressed with data grid methods that partition large genome database sets for effective use of Grid systems. BIOSCI/Bionet, a network of biology news and discussion, is approaching its third decade of service to the life sciences community. This project will maintain and improve Bionet news for several model organism communities, and areas of molecular methods, bio-software, microbiology, proteins, plant biology and others. The Bio-mirror project for distribution of large genomic and biology databanks is administered under this project, and provides infrastructure for effective genome database analyses. This project improves overall access to life sciences knowledge for all citizens. It aids the education of a broad spectrum of scientists, students and the general public, consistent with national and industry goals of teaching and research in biology and informatics. The project is a component of the infrastructure of bioinformatics in the US and worldwide, and improves partnerships with Asian-Pacific, African, European and western hemisphere nations. BIOSCI/Bionet news, IUBio Archive and Bio-Mirror projects will continue a multi-decade record of serving the world community with public access to biology information.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
Choi, JH; Kim, S; Tang, H; Andrews, J; Gilbert, DG; Colbourne, JK. "A machine-learning approach to combined evidence validation of genome assemblies," BIOINFORMATICS, v.24, 2008, p. 744-750.
Clark, AG; Eisen, MB; Smith, DR; Bergman, CM; Oliver, B; Markow, TA; Kaufman, TC; Kellis, M; Gelbart, W; Iyer, VN; Pollard, DA; Sackton, TB; Larracuente, AM; Singh, ND; Abad, JP; Abt, DN; Adryan, B; Aguade, M; Akashi, H; Anderson, WW; Aquadro, CF; Ardell,. "Evolution of genes and genomes on the Drosophila phylogeny," NATURE, v.450, 2007, p. 203-218.
Gilbert, DG. "DroSpeGe: rapid access database for new Drosophila species genomes," NUCLEIC ACIDS RESEARCH, v.35, 2007, p. D480-D485.
Stark, A; Lin, MF; Kheradpour, P; Pedersen, JS; Parts, L; Carlson, JW; Crosby, MA; Rasmussen, MD; Roy, S; Deoras, AN; Ruby, JG; Brennecke, J; Hodges, E; Hinrichs, AS; Caspi, A; Park, SW; Han, MV; Maeder, ML; Polansky, BJ; Robson, BE; Aerts, S; van Helden,. "Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures," NATURE, v.450, 2007, p. 219-232.
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