Introduction for BEAM Ecological Niche Modeling Working Meeting Deana Pennington University of New...
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Transcript of Introduction for BEAM Ecological Niche Modeling Working Meeting Deana Pennington University of New...
Introduction for BEAM Ecological Niche Modeling
Working Meeting
Deana PenningtonUniversity of New Mexico
December 14, 2004
SEEK Project•NSF-funded•Information Technology Research (ITR)•5 years (starting year 3)•50+ researchers and developers•9 institutions
Grand Challengesin Ecology
Alterations in biodiversity…exotic species, infectious disease
Altered biogeochemical cycles at multiple spatial scales
Climate change and variability, including ecosystem reponse to change
Coupled human-natural ecosystems
Ecoinformatics
200+ years of data collection in US, 300+ globally Large and widely distributed data sets Data heterogeneity (text, Excel, GIS, DB, etc.) New data collection techniques: in situ sensor arrays Remotely-sensed imagery Scaling issues: space, time, levels (taxon)
Tackling these question will require the use of all of the information available to us
Biodiversity and ecosystem informatics R&D has been identified as a critical national priority
–Computer-mediated collaboration
–New tools for synthetic understanding
Science and Technology
Data-intensiveData mining
Bio-inspired algorithmsExp. Data Analysis
Visualization
Compute-intensiveParallel processing
High throughputGrid technologies
Domain-intensiveUser interfaces
Human cognitionOntologies
Semantic mediation
Analysis & Modeling
EcoGrid
Technologic Systems
for Scientists
Data-intensive
Compute-intensive
Domain-intensive
Science-focused
Technology-enabledScience
KeplerWorkflowSystem
Informatics and the Research Cycle
MentalModel
ResearchDesign
ShareResults
Data-intensiveData mining
Bio-inspired algs.Exp. Data Analysis
Visualization
Compute-intensive
Parallel processingHigh throughput
Grid technologies
Domain-intensive
User interfacesHuman cognition
OntologiesSem. mediation
CollectData
Inductive, DescriptiveStatistics
Deductive, PrescriptiveMechanistic
ConductAnalyses
Metadata
Scientific Workflow
Source: NIH BIRN (Jeffrey Grethe, UCSD)Source: NIH BIRN (Jeffrey Grethe, UCSD)
Promoter Identification Workflow (PIW)
Source: Matt Coleman (LLNL)Source: Matt Coleman (LLNL)
Species Distribution Workflow
Training sample
GARPrule set
Test sample
Species pres. & abs.
points
EcoGridQuery
EcoGridQuery
LayerIntegration
SampleData
+A3+A2
+A1
ModelCalculation
MapGeneration
Validation
User
Model qualityparameters
Native range prediction map
Env. layers
GenerateMetadata
ArchiveTo Ecogrid
Selectedprediction
maps
PhysicalTransformat
ion
Scaling
EcoGridDataBase
EcoGridDataBase
EcoGridDataBase
EcoGridDataBase
Integrated layers
Integrated layers
GARPrule set
Species pres. & abs.
points
ENM workflows
Climate change Species invasion Macroanalysis Cross-validation Calibration Environmental monitoring Time-specific predictions Zoonotic disease
Past year
ConceptualWorkflows
ExecutableWorkflows
Scripting/Visual modeling Single environment Single platform
Workflows: Cross-platform Cross-environment Distributed data &
analyses
Data & Analysis Sharing:EcoGrid
What is a workflow?
ReportingSharing
Research Design
•Data integration•Analysis integration (data transformation)
Starting point: Ptolemy II
Edward Lee et al. http://ptolemy.eecs.berkeley.edu/ptolemyII
Kepler Additions
Grid-enabled data and analysis sharing Local Shared Web application Web service
Statistical library: R (open source) GIS library: GDAL/GRASS (open source) Domain specific functionality (GARP, etc.)
KeplerContributors, Projects, Sponsors
Ilkay Altintas SDM Chad Berkley SEEK Shawn Bowers SEEK Tobin Fricke ROADNet Jeffrey Grethe BIRN Christopher H. Brooks Ptolemy II Zhengang Cheng SDM Dan Higgins SEEK Efrat Jaeger GEON Matt Jones SEEK Edward A. Lee Ptolemy II Kai Lin GEON Ashraf Memon GEON Bertram Ludaescher BIRN, GEON,
SDM, SEEK Steve Mock NMI Steve Neuendorffer Ptolemy II Jing Tao SEEK Mladen Vouk SDM Xiaowen Xin SDM Yang Zhao Ptolemy II Bing Zhu SEEK •••
E-Science Link-up Project
Recommended for NEON
Agenda
Goal: To give you the knowledge and training needed to begin to develop grid-enabled applications in Kepler
Prototype project: ENM Mammal Project Resource sharing and grid technologies (Tues am) Metadata requirements (Tues pm) Kepler training (Wed am) Kepler applications in ENM
What you can do now (or very soon) (Wed am/pm) What expanded functionality needs to be added (Thurs am/pm)
Feedback and planning (Thurs pm)
Important Disclaimer
Kepler is a CIS research project in its EARLY stage… there are many, many still to be done. If: Something crashes….it’s a work in progress Something looks weird…it’s a work in progress Something doesn’t work…it’s a work in
progress Something should be done a different way…it’s
a work in progress best to keep a sense of humor
Acknowledgements
This material is based upon work supported by the National Science Foundation under awards 0225676 for SEEK and 0225673 (AWSFL008-DS3) for GEON and by the Department of Energy under Contract No. DE-FC02-01ER25486 for SciDAC/SDM and by DARPA under Contract No. F33615-00-C-1703 for Ptolemy. Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF).
The National Center for Ecological Analysis and Synthesis, a Center funded by NSF (Grant Number 0072909), the University of California, and the UC Santa Barbara campus.
The Andrew W. Mellon Foundation.
PBI Collaborators: NCEAS, University of New Mexico (Long Term Ecological Research Network Office), San Diego Supercomputer Center, University of Kansas (Center for Biodiversity Research)
Kepler contributors: SEEK, Ptolemy II, SDM/SciDAC, GEON