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openModeller

Presentation Plan:

Overview of openModeller

OMWS: an open standard for distributed ecological niche modelling

openModeller in relation to TDWG

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openModeller Overview

Project started by CRIA, Brazil in 2003

An Open Source project hosted on sourceforge

Written in C++ with SWIG language bindings

Provides an environment for carrying out fundamental ecological niche modelling

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openModeller Architecture

libopenmodeller is the core component

Provides data IO for gdal supported raster formats

Seamlessly manages rasters in different formats

Handles sampling of rasters at occurrence sites

Writes model outputs to raster files

Algorithm plugins

Algorithm plugins extend the library with support for various ecological niche modelling implementations

GARP, Bioclim, CSM etc are already implemented

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openModeller Architecture

openModeller DesktopA graphical user interface for openModeller

Version 0 : A wizard based gui (stable version)

Version 1: A traditional desktop application (unstable)

openModeller console interface also available

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openModeller, open architecture

Client(e.g. openModeller Desktop)

Modelling Engine(libopenmodeller)

Modelling Algorithm(e.g. GARP)

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openModeller, distributed,open architecture

Client(e.g. openModeller Desktop)

Modelling Engine(libopenmodeller)

Modelling Algorithm(e.g. GARP)

SOAP Client Layer

SOAP Server

Internet

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Modelling Engine(libopenmodeller)

Modelling Algorithm(e.g. GARP)

Modelling Engine(libopenmodeller)

Modelling Algorithm(e.g. GARP)

openModeller, distributed,open architecture

Client(e.g. openModeller Desktop)

Modelling Engine(libopenmodeller)

Modelling Algorithm(e.g. GARP)

SOAP Client Layer

SOAP Server

Internet

Condor

Clu

ster

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openModeller, distributed,open architecture

Client(e.g. openModeller Desktop)

Modelling Engine(MaxEnt)

SOAP Client Layer

SOAP Server

Internet

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openModeller WSI

Using SOAP (Document / Literal)

Separate XML Schema for types & elements

API is very simple (few methods)

Prototype implementation: gSOAP on server side, Perl with SOAP:Lite on client side (console) and gSOAP on client side (GUI).

Protocol not specific to openModeller

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getLayers()

Used to determine what environmental layers are on the server.

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getLayers()

Presented to user as heirachical tree

Layers have identifiers that could resolve files, database urls (WCS in the future)

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getAlgorithms()

Used to determine what modelling algorithms are on the server.

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getAlgorithms()

Presented to user as list

Users can set parameter values

Document includes descriptive data to aid user decision making

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createModel()

Uses locality, algorithm and layer data to invoke a model creation job on the server -> Job Ticket

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createModel()

Returns a serialised model definition document

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projectModel()

Used to render a probaility of occurence map

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getMapAsUrl()

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Additional Methodsping()

getProgress()

getLog()

getMapAsUrl()

getMapAsAttachment()

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Integration With TDWG/OGCAutomated resolution of taxonomy (GBIF Portal)

Automated retrieval of occurrence data (WFS + GML)

Metadata - Provenance of models (what species was used for this model, using which data from which institutions etc) (OGC)

Access to environment data via WCS

APIs for analysis (missing from TDWG)

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Acknowledgements

More Infohttp://openmodeller.sf.net

CRIA, Brazil (http://cria.org.br)FAPESP, Brazil

(http://www.fapesp.br)