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  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-intensive Data mining Bio-inspired algorithms Exp. Data Analysis Visualization Compute-intensive Parallel processing High throughput Grid technologies Domain-intensive User interfaces Human cognition Ontologies Semantic mediation Analysis & Modeling EcoGrid

Technologic Systems for Scientists Data-intensive Compute- intensive Domain- intensive Science-focused Technology-enabled Science Kepler Workflow System

Informatics and the Research Cycle Mental Model Research Design Share Results Data-intensive Data mining Bio-inspired algs. Exp. Data Analysis Visualization Compute- intensive Parallel processing High throughput Grid technologies Domain- intensive User interfaces Human cognition Ontologies Sem. mediation Collect Data Inductive, Descriptive Statistics Deductive, Prescriptive Mechanistic Conduct Analyses Metadata Scientific Workflow

Source: NIH BIRN (Jeffrey Grethe, UCSD)

Promoter Identification Workflow (PIW) Source: Matt Coleman (LLNL)

Species Distribution Workflow Training sample GARP rule set Test sample Species pres. & abs. points EcoGrid Query EcoGrid Query Layer Integration Sample Data + A3 + A2 + A1 Model Calculation Map Generation Validation User Model quality parameters Native range prediction map Env. layers Generate Metadata Archive To Ecogrid Selected prediction maps Physical Transformation Scaling EcoGrid DataBase EcoGrid DataBase EcoGrid DataBase EcoGrid DataBase Integrated layers Integrated layers GARP rule set Species pres. & abs. points

ENM workflows  Climate change  Species invasion  Macroanalysis  Cross-validation  Calibration  Environmental monitoring  Time-specific predictions  Zoonotic disease

Past year Conceptual Workflows Executable Workflows  Scripting/Visual modeling Single environment Single platform  Workflows: Cross-platform Cross-environment Distributed data & analyses

Data & Analysis Sharing: EcoGrid

What is a workflow? Reporting Sharing Research Design Data integration Analysis integration (data transformation)

Starting point: Ptolemy II Edward Lee et al.

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.)

Kepler Contributors, 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 for SEEK and (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. F 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 ), 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