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.
Gene structures and information of several animal and plants are discovered through construction of genome and expressed sequences, including Pea aphid (plant pest), Water flea (fresh water health indicator), Deer tick (human disease vector), Jewel wasp (beneficial insect), Chocolate tree (tasty but troubled by disease and climate), Loblolly pine tree (forest values). This project provides new developments in genome database informatics and cyber-infrastructure to several bioscience communities for discovering genomes and gene-environment interactions (http://eugenes.org/EvidentialGene/). It also supports public biology news, data sharing and information services (http://www.bio.net and http://bio-mirror.net). New methods that determine high quality gene information have been developed and published for others to use. Resulting gene structures and descriptions of several animals and plants are placed into public databases that will continue for many years as a basis of new discoveries by scientists, biomedical and agricultural researchers. A basic engineering discovery of this work overturns dogma that genes must be determined from genome assemblies; instead genes can be better determined from expressed gene sequences. Impacts of this work today and in future include: discovering genetic responses to environmental health impacts of man-made or natural toxins to the aquatic sentinel water flea; improvements to sustainable agricultural through understanding plant disease resistances and other traits that aid farmers around the world; better understanding of genetic interactions of human disease vectors and agriculturally beneficial and pest bugs such as aphids, ticks, bees and wasps.
