Madey, G.R., Cabaniss, S.E., Maurice, P.A., Xiang, X., Arthurs, L., Kennedy, R., Huang, Y
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Transcript of Madey, G.R., Cabaniss, S.E., Maurice, P.A., Xiang, X., Arthurs, L., Kennedy, R., Huang, Y
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Online Collaboratory for NOM Research: Agent-based Simulations, Data-Mining,
and Knowledge-DiscoveryMadey, G.R., Cabaniss, S.E., Maurice, P.A., Xiang, X., Arthurs, L., Kennedy, R., Huang, Y
University of Notre Dame
University of New Mexico
ASLO 2005
February 24, 2005
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Overview
Project Background E-Science Background The NOM e-Science Collaboratory Invitation to Test, Contribute, Participate Summary
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Background
Small NSF-ITR involving Computer Scientists and Environmental Scientists
Focus: “Stochastic Synthesis: Simulating the environmental transformations of NOM”
IT Focus: e-Science, Web-Based Science, Agent-Based Simulation, Data Mining
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E-Science Background
NSF Cyberinfrastructure Program Sensor networks Large amounts of data => discovery through
datamining Online linked data repositories Online analysis programs: search, extraction,
matching, simulation, visualizations, etc.
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E-Science Background (cont) WWW Telescope Virtual Observatories
NASA Skyview US National Virtual Observatory International Virtual Observatory Alliance
More and more research done without every using a telescope => use of distributed data already collected
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E-Science Background (cont) NCBI (National Center for
Biotechnology Information)
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Model Organism e-Science Sites
FlyBase: Drosophila WormBase: C. elegans VectorBase: Mosquitos Mouse Genome DictyBase Etc. So many => GMOD
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Questions?
Has this research community begun to participate in the e-Science initiatives?
Would this community benefit from e-Science initiatives?
Is this community interested in an e-Science initiatives?
Is this community willing to experiment?
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The NOM e-Science Collaboratory
Web-based Back-end database A cluster of simulation servers Shared simulation results Shared simulation configurations Other collaboratory features
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http://www.nd.edu/~nom
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Software download/online
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Simulation HomePage: http://tobit.cse.nd.edu/
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Reaction Batch Model
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Agent-Based Modeling of NOM
NOMHumic substances& small organics
NOMHumic substances& small organics
CO2CO2
Cellulose
Lignins
Proteins
Cutins
Lipids
Tannins
O2
lightbacteriaH+, OH-
metalsfungi
O2
lightbacteriaH+, OH-
metalsfungi
O2
lightbacteriaH+, OH-
metalsfungi
Goal: A widely available, testable, mechanistic model of NOM evolution in the environment.
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Data model
Pseudo-Molecule
Elemental Functional StructuralComposition
CalculatedChemical Properties
and Reactivity
LocationOriginState
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Environmental Parameters
Physical:Temperature
Light Intensity
Chemical:Water
pH[O2]
Biological:Bacterial DensityOxidase ActivityProtease Activity
Decarboxylase Activity
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Invitation to Test, Contribute, Participate
HTTP://www.nd.edu/~nom/ HTTP://tobit.cse.nd.edu/
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Summary Growing phenomenon of e-Science based
research One small “environmental science” e-Science
site: http://tobit.cse.nd.edu Invitation to test, download, evaluate,
contribute, build your own, etc. Description of Agent-based NOM Simulator
(downloadable and online) by Steve Cabaniss next!