Parallelizing the Protein Threading Problem in a Hybrid Peer-to-Peer Based High Performance Computing Platform

Author

Luo, Fei ; Chen, Lin

Author_Institution

Sch. of Inf. & Eng., Eastern China Univ. of Sci. & Technol., Shanghai, China

fYear

2009

fDate

1-3 June 2009

Firstpage

136

Lastpage

141

Abstract

The protein threading problem (PTP) is to determine the three-dimensional structure of a given protein sequence. Currently its serial resolutions are time-consuming and data-intensive. Nevertheless, the parallel and distributed systems offer opportunities to improve the efficiency of PTP by releasing its computational bottleneck. Therefore, a 1-level-core parallel threading algorithm is proposed and implemented in a hybrid peer-to-peer (P2P) based high performance computing (HPC) platform, P2HP-2. Through experiments and analysis, it shows that high performance can be achieved through the 1-level-core parallel algorithm in P2HP-2.

Keywords

biology computing; multi-threading; peer-to-peer computing; proteins; 1 level-core parallel threading algorithm; distributed systems; hybrid peer-to-peer based high performance computing platform; parallel systems; protein sequence; protein threading problem; Computational complexity; Concurrent computing; Distributed computing; High performance computing; Information science; Middleware; Parallel algorithms; Peer to peer computing; Protein engineering; Protein sequence; high performance computing; parallel protein threading; peer-to-peer computing;

fLanguage

English

Publisher

ieee

Conference_Titel

Computer and Information Science, 2009. ICIS 2009. Eighth IEEE/ACIS International Conference on

Conference_Location

Shanghai

Print_ISBN

978-0-7695-3641-5

Type

conf

DOI

10.1109/ICIS.2009.154

Filename

5223099