HPC AND GRID COMPUTING FOR INTEGRATIVE BIOMEDICAL RESEARCH

被引：8

作者：

Kurc, Tahsin ^{[1
]}

Hastings, Shannon ^{[2
]}

Kumar, Vijay ^{[2
,3
]}

Langella, Stephen ^{[2
]}

Sharma, Ashish ^{[1
]}

Pan, Tony ^{[1
]}

Oster, Scott ^{[2
]}

Ervin, David ^{[2
]}

Permar, Justin ^{[2
]}

Narayanan, Sivaramakrishnan ^{[2
,3
]}

Gil, Yolanda ^{[4
]}

Deelman, Ewa ^{[4
]}

Hall, Mary ^{[5
]}

Saltz, Joel ^{[1
]}

机构：

[1] Emory Univ, Ctr Comprehens Informat, Atlanta, GA 30322 USA

[2] Ohio State Univ, Dept Biomed Informat, Columbus, OH 43210 USA

[3] Ohio State Univ, Dept Comp Sci & Engn, Columbus, OH 43210 USA

[4] Univ So Calif, Inst Informat Sci, Los Angeles, CA 90292 USA

[5] Univ Utah, Coll Comp, Cedar City, UT 84720 USA

来源：

INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS | 2009年 / 23卷 / 03期

基金：

美国国家科学基金会;

关键词：

integrative biomedical research; system level integrative analysis; multi-scale integrative investigation; INFRASTRUCTURE; ARCHITECTURE; DESIGN;

D O I：

10.1177/1094342009106192

中图分类号：

TP3 [计算技术、计算机技术];

学科分类号：

0812 ;

摘要：

Integrative biomedical research projects query, analyze, and integrate many different data types and make use of datasets obtained from measurements or simulations of structure and function at multiple biological scales. With the increasing availability of high-throughput and high-resolution instruments, the integrative biomedical research imposes many challenging requirements on software middleware systems. In this paper, we look at some of these requirements using example research pattern templates. We then discuss how middleware systems, which incorporate Grid and high-performance computing, could be employed to address the requirements.

引用

页码：252 / 264

页数：13

共 25 条

[1]

Alexander C., 1977, A Pattern Language

[2] Distributed processing of very large datasets with DataCutter [J].

Beynon, MD ;

Kurc, T ;

Catalyurek, U ;

Chang, CL ;

Sussman, A ;

Saltz, J .

PARALLEL COMPUTING, 2001, 27 (11) :1457-1478

[3] caCORE: A common infrastructure for cancer informatics [J].

Covitz, PA ;

Hartel, F ;

Schaefer, C ;

De Coronado, S ;

Fragoso, G ;

Sahni, H ;

Gustafson, S ;

Buetow, KH .

BIOINFORMATICS, 2003, 19 (18) :2404-2412

[4]

Deelman E, 2004, LECT NOTES COMPUT SC, V3165, P11

[5] Modeling and managing state in distributed systems: The role of OGSI and WSRF [J].

Foster, I ;

Czajkowski, K ;

Ferguson, DF ;

Frey, J ;

Graham, S ;

Maguire, T ;

Snelling, D ;

Tuecke, S .

PROCEEDINGS OF THE IEEE, 2005, 93 (03) :604-612

[6]

Gamma Erich., 1994, DESIGN PATTERNS

[7]

GIL Y, 2007, 19 ANN C INN APPL AR

[8]

Han J, 2008, CANCER INFORM, V6, P111

[9] Introduce: An open source toolkit for rapid development of strongly typed grid services [J].

Hastings S. ;

Oster S. ;

Langella S. ;

Ervin D. ;

Kurc T. ;

Saltz J. .

J. Grid Comput., 2007, 4 (407-427) :407-427

[10]

Hill E. F., 2003, Jess in action: Java rule-based systems

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