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2015 ; 26
(7-9
): 577-93
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Development of an informatics infrastructure for data exchange of biomolecular
simulations: Architecture, data models and ontology
#MMPMID26387907
Thibault JC
; Roe DR
; Eilbeck K
; Cheatham TE III
; Facelli JC
SAR QSAR Environ Res
2015[]; 26
(7-9
): 577-93
PMID26387907
show ga
Biomolecular simulations aim to simulate structure, dynamics, interactions, and
energetics of complex biomolecular systems. With the recent advances in hardware,
it is now possible to use more complex and accurate models, but also reach time
scales that are biologically significant. Molecular simulations have become a
standard tool for toxicology and pharmacology research, but organizing and
sharing data - both within the same organization and among different ones -
remains a substantial challenge. In this paper we review our recent work leading
to the development of a comprehensive informatics infrastructure to facilitate
the organization and exchange of biomolecular simulations data. Our efforts
include the design of data models and dictionary tools that allow the
standardization of the metadata used to describe the biomedical simulations, the
development of a thesaurus and ontology for computational reasoning when
searching for biomolecular simulations in distributed environments, and the
development of systems based on these models to manage and share the data at a
large scale (iBIOMES), and within smaller groups of researchers at laboratory
scale (iBIOMES Lite), that take advantage of the standardization of the meta data
used to describe biomolecular simulations.