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