Name
Abstract | ||
|---|---|---|
The ongoing global effort of genome sequencing is making large scale comparative proteomic analysis an intriguing task. The Encyclopedia of Life (EOL; http://eol.sdsc.edu) project aims to provide current functional and structural annotations for all available proteomes, a computational challenge never seen before in biology. Using an integrative genome annotation pipeline (iGAP), we have produced 3D models and functional annotations for more than 100 proteomes thus far. This process is greatly facilitated by grid compute resources, and especially by the development of grid application execution environment. AppLeS (Application-Level Scheduling) Parameter Sweep Template (APST) has been adopted by the EOL project as a mediator to grid middleware. APST has made the annotation process much more efficient, highly automated and scalable. Currently we are building a domain-specific bioinformatics workflow management system (BWMS) on top of APST, which further streamlines grid deployment of life science applications. With these developments in mind, we discuss some common problems and expectations of grid computing for high throughput proteomics. |
Year | DOI | Venue |
|---|---|---|
2004 | 10.1007/BF03040951 | New Generation Comput. |
Keywords | Field | DocType |
grid middleware,life project,igap,grid computing,genome sequencing,annotation process,available proteomes,integrative genome annotation pipeline,grid application execution environment,eol project,eol,grid,functional annotation,bioinformatics,streamlines grid deployment,grid software,apst,encyclopedia of life,workflow management system,genome sequence,high throughput,genome annotation | World Wide Web,Programming language,Grid computing,Annotation,Software deployment,Software engineering,Genome project,Computer science,Encyclopedia of Life,Grid,Scalability,Bioinformatics workflow management system | Journal |
Volume | Issue | ISSN |
22 | 2 | 1882-7055 |
Citations | PageRank | References |
13 | 0.87 | 18 |
Authors | ||
16 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Wilfred W. Li | 1 | 413 | 29.22 |
| Robert W. Byrnes | 2 | 18 | 1.69 |
| Jim Hayes | 3 | 859 | 70.24 |
| Adam Birnbaum | 4 | 104 | 9.96 |
| Vicente M. Reyes | 5 | 13 | 0.87 |
| Atif Shahab | 6 | 25 | 2.95 |
| Coleman Mosley | 7 | 13 | 0.87 |
| D. Pekurovsky | 8 | 116 | 9.60 |
| Greg B. Quinn | 9 | 237 | 15.95 |
| I. Shindyalov | 10 | 173 | 26.92 |
| H. Casanova | 11 | 1064 | 60.15 |
| Larry Ang | 12 | 17 | 1.68 |
| Francine Berman | 13 | 2251 | 220.90 |
| Peter W. Arzberger | 14 | 92 | 10.87 |
| Mark Miller | 15 | 96 | 12.57 |
| Henri Casanova | 16 | 1671 | 106.43 |