The encyclopedia of life project: Grid software and deployment

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 (iQAP), 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

Recent Advances in Solving the Protein Threading Problem

“…For example, the encyclopedia of life project [15] integrates 123D+ threading package in its distributed pipeline. All the pipeline processes, from DNA sequence to protein structure modeling, are parallelized by a grid application execution environment called APST (for Application-level scheduling Parameter Sweep Template).…”

Biological sequence alignment on the computational grid using the GrADS framework

“…In one example scenario, all-to-all genome alignments over multiple databases can be used to study phylogeny. In another example that could benefit from data locality, the Encyclopedia of Life (EOL) project [18] seeks to characterize all proteins encoded by publicly available genomes through putative assignment of structures models and functions.…”

GridSAT: Design and Implementation of a Computational Grid Application

“…These resource aggregations can be harnessed by Grid applications to solve problems in science and engineering [8,9] which require large computing power. Solving such challenging problems and enabling new scientific results is an integral part of the Grid computing vision.…”