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Title: Computing through Scientific Abstractions in SysBioPS

Abstract

Today, biologists and bioinformaticists have a tremendous amount of computational power at their disposal. With the availability of supercomputers, burgeoning scientific databases and digital libraries such as GenBank and PubMed, and pervasive computational environments such as the Grid, biologists have access to a wealth of computational capabilities and scientific data at hand. Yet, the rapid development of computational technologies has far exceeded the typical biologist’s ability to effectively apply the technology in their research. Computational sciences research and development efforts such as the Biology Workbench, BioSPICE (Biological Simulation Program for Intra-Cellular Evaluation), and BioCoRE (Biological Collaborative Research Environment) are important in connecting biologists and their scientific problems to computational infrastructures. On the Computational Cell Environment and Heuristic Entity-Relationship Building Environment projects at the Pacific Northwest National Laboratory, we are jointly developing a new breed of scientific problem solving environment called SysBioPSE that will allow biologists to access and apply computational resources in the scientific research context. In contrast to other computational science environments, SysBioPSE operates as an abstraction layer above a computational infrastructure. The goal of SysBioPSE is to allow biologists to apply computational resources in the context of the scientific problems they are addressing and the scientific perspectives frommore » which they conduct their research. More specifically, SysBioPSE allows biologists to capture and represent scientific concepts and theories and experimental processes, and to link these views to scientific applications, data repositories, and computer systems.« less

Authors:
; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
15017451
Report Number(s):
PNNL-SA-42055
TRN: US200517%%390
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Conference
Resource Relation:
Conference: Proceedings of the 2004 IEEE International Conference on Systems, Man and Cybernetics , 1:70-75
Country of Publication:
United States
Language:
English
Subject:
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; AVAILABILITY; BIOLOGY; COMPUTERS; CYBERNETICS; EVALUATION; INFORMATION SYSTEMS; INFORMATION DISSEMINATION; problem-solving environments; visual modeling; scientific workflow; scientific computing

Citation Formats

Chin, George, Stephan, Eric G., and Gracio, Deborah K. Computing through Scientific Abstractions in SysBioPS. United States: N. p., 2004. Web.
Chin, George, Stephan, Eric G., & Gracio, Deborah K. Computing through Scientific Abstractions in SysBioPS. United States.
Chin, George, Stephan, Eric G., and Gracio, Deborah K. Wed . "Computing through Scientific Abstractions in SysBioPS". United States.
@article{osti_15017451,
title = {Computing through Scientific Abstractions in SysBioPS},
author = {Chin, George and Stephan, Eric G. and Gracio, Deborah K.},
abstractNote = {Today, biologists and bioinformaticists have a tremendous amount of computational power at their disposal. With the availability of supercomputers, burgeoning scientific databases and digital libraries such as GenBank and PubMed, and pervasive computational environments such as the Grid, biologists have access to a wealth of computational capabilities and scientific data at hand. Yet, the rapid development of computational technologies has far exceeded the typical biologist’s ability to effectively apply the technology in their research. Computational sciences research and development efforts such as the Biology Workbench, BioSPICE (Biological Simulation Program for Intra-Cellular Evaluation), and BioCoRE (Biological Collaborative Research Environment) are important in connecting biologists and their scientific problems to computational infrastructures. On the Computational Cell Environment and Heuristic Entity-Relationship Building Environment projects at the Pacific Northwest National Laboratory, we are jointly developing a new breed of scientific problem solving environment called SysBioPSE that will allow biologists to access and apply computational resources in the scientific research context. In contrast to other computational science environments, SysBioPSE operates as an abstraction layer above a computational infrastructure. The goal of SysBioPSE is to allow biologists to apply computational resources in the context of the scientific problems they are addressing and the scientific perspectives from which they conduct their research. More specifically, SysBioPSE allows biologists to capture and represent scientific concepts and theories and experimental processes, and to link these views to scientific applications, data repositories, and computer systems.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Wed Oct 13 00:00:00 EDT 2004},
month = {Wed Oct 13 00:00:00 EDT 2004}
}

Conference:
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