GEON: The User Perspective

Choonhan Youn

Dogan Seber, Chaitan Baru, Ashraf Memon

San Diego Supercomputer Center,

University of California at San Diego

GEON (GEOscience Network)GEON (GEOscience Network)• A cyberinfrastructure project for geosciences

funded by NSF ITR.• creating an IT infrastructure to “enable”

interdisciplinary geoscience research -- not a group of researchers, but the entire community will benefit

• Vision: Enable new discoveries in the geosciences by building an easy-to-use and “comprehensive” data, software, tools, and information network by utilizing state-of the-art information technology resources.

Current GEON member institutionsCurrent GEON member institutionsMembers• Arizona State University• Bryn Mawr College• Penn State University• Rice University• San Diego State University• San Diego Supercomputer Center /

University of California, San Diego• University of Arizona• University of Idaho• University of Missouri, Columbia• University of Texas at El Paso• University of Utah• Virginia Tech• UNAVCO, Inc.• Digital Library for Earth System Education

(DLESE)

Partners• California Institute for Telecommunications

and Information Technology Cal-IT2• Chronos• CUAHSI• ESRI• Geological Survey of Canada• Georeference Online• IBM• Kansas Geological Survey• Lawrence Livermore National Laboratory• U.S. Geological Survey (USGS)

Other Affiliates• Southern California Earthquake Center

(SCEC), EarthScope, IRIS, NASA

GEOSCIENCE CHALLENGESGEOSCIENCE CHALLENGES• Exponential Increase in Data Volume

– How to manage vast amounts of data can be used by all scientists in an easy-to-use environment

• Data Storage, Access and Preservation– How to build a framework to exchange data and help preserving collected data sets

• Data Integration (semantic and syntactic)– How to merge multiple geology maps to make a seamless (“integrated”) map

• Computational Challenges – How to build a system that helps scientists run advance software without having

access to significant resources (computers and technical), focusing on the science problem

• Advance Visualization (3D/4D)– How to build a visualization system that helps scientists analyze large and complex

data sets dynamically

• Archiving and publications of results with reusable components (reusability)– How to preserve scientific results and help others to repeat the analysis as efficiently

as possible?

GEON Cyberinfrastructure (CI) Principles• CI: Support the “day to day” conduct of science (e-

science), in addition to “hero” computations• An equal partnership

– IT works in close conjunction with science• Create shared “science infrastructure”

– Integrated online databases, with advanced search and query engines

– Online models, robust tools and applications• Leverage from other intersecting projects

– Much commonality in the technologies, regardless of science disciplines, e.g. BIRN, SEEK, and many others

Main e-Research facilities I• A Resource Registration System for Data Providers

– Register ontologies (domain knowledge) and ontology articulations– Register datasets with metadata including data access information– Optionally register datasets to ontologies (which is crucial for data

integration and smart search): Ontology enabled semantic integration– Shapefile, ASCII, Excel, GMT Raster, Geo TIFF, Relational Database, PDF,

tool, WMS service, Web service, etc.

• A Search Engine for Data Users– Metadata based search– Spatial coverage based search– Temporal coverage based search– Concept based search– Ontology based data discovering

Main e-Research facilities II• The user workspace, called myGEON area.

– Users are able to search and collect their data sets from the GEON search engine and integrate them.

– For example, users can review and analyze "SYNSEIS“ ouputs that are generated by job running.

• Computational HPC– SYNSEIS (Synthetic Seismogram toolkit)

• Workflow– LiDAR: an end-to-end solution for the distribution, interpolation

and analysis of LiDAR / ALSM point data. – Atype workflow: generates map for all plutonic bodies in

Virginia from the VA Igneous rocks database based on the certain inputs.

Constraints for main e-Research facilities

• Dynamic workflow issues due to the web-based system on the GEON

• Large computational clusters for simulating GEON applications as needed– GEON has three small cluster nodes on partner sites

GEON Portal Usability• Easy of use

– GEON Search, SYNSEIS, many of them, etc.

• Make complex tasks easy to specify– LiDAR

• Highly interactive– SYNSEIS

• Integrated access to tools and resources– myGEON, Mapping Integration

Computational HPC for SYNSEIS

Lessons Learnt• Its main strengths

– Standard-compliant ways

– Using open source libraries and tools for most of implementations

• Its main weaknesses– Highly user interactive, friendly interface issues within

the portlet franework

• Would you consider alternatives to a portal solution?– Currently, No

Future Plan

• Will add and develop new functionalities based on the requests from GEON PIs and geoscience community.

• Will keep improving the portal usability.– For example, in case of SYNSEIS, add more user

capabilities in the user interface for complex earthquake simulations.

• Will expand its use within geoscience community internationally – Center on GEON PIs first

GEON: The Developer Perspective

Choonhan Youn

Dogan Seber, Chaitan Baru, Ashraf Memon

San Diego Supercomputer Center,

University of California at San Diego

Methods of GEON’s Design

• Several workshops were held with participation from scientists from different disciplines like geochemistry, geophysics etc.

• Also Principal Investigators (PIs) visits SDSC for focused discussion on their requirements

• Prototypes are built using gathered requirements and then spiral model of software development is followed to enhance the prototype.

Service-Oriented Approach

Priority of Functional and non-functional requirements

• Start with functional requirement from the principal investigators or local geo-science PI

• Prototypes are built and functional requirements are tested

• Then focus on to non-functional requirements like usability

Technical Strategy

• The “two-tier” approach– Use best practices, including use of commercial tools

and open standards, where applicable…• start with development using the technology available now

– …while developing advanced technology, and doing CS research

• push for open source and best practices as much as possible

GEONmiddleware

GEONSearch, Registration, myGEON Portlet

myOntology.owl myDataset.foo

metadatametadata

User Access (via Portal)User Access (via Portal)

Gazetteer, DLESE, …

Geologic Age, Chronos, …

external services

GEONsearchGEONsearch

Search condition(s)spatial temporal concept

LogLog

myGEON myGEON

GEON Workspace

(user)

User actionsadd delete manipulate

GEON Catalog

ResourceRegistrationResourceRegistration

SRB

Client Access (via web services)Client Access (via web services)

Other distributed apps Kepler, DLESE, …

Flash Application

SYNSEIS toolkit

SYNSEIS Portlet

Data Model Service

Job Submission/Monitoring and File Service

Data Archives Service

HPC ResourcesData Repository

Job Database

SOAP SOAP

JDBC CORBA(IIOP)Grid Services

GEONGrid Portal

User Access (via Web Browser)User Access (via Web Browser)

Cornell Map Server

IRISDMC

HTTP

SOAP SOAP

Grid FTP

Web Services

myGEON Portlet

SAC Service

TeraGrid clusters

Development Issues• Constraints

– Interoperability issues due to use of existing tools• Use of existing tools developed in Fortran and some machine dependent

algorithms and code GRASS based GIS processing.

• Incompatible implementation of same standard (OGC’s WMS)

– Usability requirements• Portlets UI is designed by the software developers and so they are not

very user friendly

– Part of our tension in the project is that • while this is an R&D project for the IT folks, the science folks want some

of it to look like production software

– lack of user input in some cases, • because some users are still trying to get up to speed with the IT concepts

so they haven’t really used the system.

Evaluation

• Usually success of our GEON services is determined by user satisfaction!

• Usability workshop was held recently with domain scientist involved and their feedback was taken.– Based on this report, we are working on it

• Another workshop will be held after the implementation of the suggested changes.

Lessons Learnt

• The most successful aspects– Integrating with other grid, such as TeraGrid

– Data registration, search capabilities for geoscience community

– Community involvement

• The least successful aspects– Community still is evaluating this system.

Future Plans

• Will provide a secure role-based authorization control (using SAML) to fully integrate into the GEON portal.

• Will add WSRP service.• The definition of conventions for managing state

may be handled through standard ways such as WSRF so that applications discover, bind, and communicate with stateful resources in standard and interoperable ways.

GEON Search Portlet

GEON Resource Registration Portlet

User Workspace

Mapping Integration Portlet

Client PortletClient Portlet Map IntegrationPortlet (Mediator)Map Integration

Portlet (Mediator)

Geon Dataset Ids

Gri

dsp

her

e

GEON Metadata Catalogue Ontology

ServiceSRB

Query Tracking

DB

QueryService

MappingServices

Web

ser

vic

es

1. Dataset Ids to Dataset Names

2. Dataset Ids to Ontology Ids

3. Ontology Ids to Ontology Names

4. Ontology Ids to Ontology Concepts

Ontology Engine ArcIMSK

no

wle

dg

e R

epre

sen

tati

on

Redefine Query

Map

pin

g

Execute Query

Download DatasetsStore Query Results

Query Result Indexing

Generate Map

GET_EXTRACT

GET_MAP

IBM DB2

GEON Portal

NFS Mounted Disk

Data ProcessingAlgorithms

Compute Cluster

x,y,z and attribute

raw dataprocess output

maps/data

Client

WWW

GEONSearchPortlet

LiDARProcessPortlet

OtherPortlet

LiDARProcessing

Service

LiDARProcessing

Service

SpatialQuery

Service

SpatialQuery

Service

GEONSearchService

GEONSearchService

Software Tools

DB2Spatial

FunctionGRASS ARCINFO GMT

GEON Catalog

DATA PROCESSING(LiDAR Portlet)

TeraGrid DataStar