Download PenningtonBEAM200412014intro

Introduction for
BEAM Ecological Niche
Modeling Working Meeting
Deana Pennington
University 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 Challenges
in Ecology
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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
Tackling these question will require the use of all of
the information available to us
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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)
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-intensive
Data mining
Bio-inspired algorithms
Exp. Data Analysis
Visualization
Compute-intensive
Parallel processing
High throughput
Grid technologies
EcoGrid
Analysis & Modeling
Domain-intensive
User interfaces
Human cognition
Ontologies
Semantic mediation
Technologic Systems
for Scientists
Technology-enabled
Science
Data-intensive
Science-focused
Computeintensive
Domainintensive
Kepler
Workflow
System
Informatics and
the Research Cycle
Data-intensive
Data mining
Bio-inspired algs.
Exp. Data Analysis
Visualization
Domainintensive
User interfaces
Human cognition
Ontologies
Sem. mediation
Inductive, Descriptive
Statistics
Mental
Model
Research
Design
Collect
Data
Conduct
Analyses
Share
Results
Metadata
Deductive, Prescriptive
Mechanistic
Computeintensive
Parallel processing
High throughput
Grid technologies
Scientific Workflow
Source: NIH BIRN (Jeffrey Grethe, UCSD)
Promoter Identification
Workflow (PIW)
Source: Matt Coleman (LLNL)
Species Distribution Workflow
EcoGrid
DataBase
Species
pres. & abs.
points
Species
pres. & abs.
points
Test sample
+A2
+A3
EcoGrid
Query
Physical
Transformation
Sample
Data
EcoGrid
DataBase
Training
sample
GARP
rule set
Model
Calculation
Validation
GARP
rule set
Integrated
layers
Env.
layers
EcoGrid
DataBase
EcoGrid
Query
EcoGrid
DataBase
Model quality
parameters
+A1
Integrated
layers
Layer
Integration
Native range
prediction map
Map
Generation
User
Selected
prediction
maps
Scaling
Archive
To Ecogrid
Generate
Metadata
ENM workflows
Climate change
 Species invasion
 Macroanalysis
 Cross-validation
 Calibration
 Environmental monitoring
 Time-specific predictions
 Zoonotic disease
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Past year
Conceptual
Workflows
Executable
Workflows
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Scripting/Visual modeling
 Single environment
 Single platform
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Workflows:
 Cross-platform
 Cross-environment
 Distributed data &
analyses
Data & Analysis Sharing:
EcoGrid
What is a workflow?
Research Design
•Data integration
•Analysis integration (data transformation)
Reporting
Sharing
Starting point: Ptolemy II
Edward Lee et al. http://ptolemy.eecs.berkeley.edu/ptolemyII
Kepler Additions
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Grid-enabled data and analysis sharing
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Local
Shared
Web application
Web service
Statistical library: R (open source)
GIS library: GDAL/GRASS (open source)
Domain specific functionality (GARP, etc.)
Kepler
Contributors, Projects, Sponsors
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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
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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
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Prototype project: ENM Mammal Project
Resource sharing and grid technologies (Tues am)
Metadata requirements (Tues pm)
Kepler training (Wed am)
Kepler applications in ENM
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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
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Kepler is a CIS research project in its
EARLY stage… there are many, many still
to be done. If:
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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-FC0201ER25486 for SciDAC/SDM and by DARPA under Contract No. F33615-00C-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