openModeller

1
openModeller

• Presentation Plan
• Overview of openModeller
• OMWS an open standard for distributed ecological
  niche modelling
• openModeller in relation to TDWG

2
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

3
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

4
openModeller Architecture

• openModeller Desktop
• A 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

5
openModeller, open architecture
Client(e.g. openModeller Desktop)
Modelling Engine (libopenmodeller)
Modelling Algorithm (e.g. GARP)
6
openModeller, distributed,open architecture
Client(e.g. openModeller Desktop)
SOAP Server
Modelling Engine (libopenmodeller)
SOAP Client Layer
Modelling Algorithm (e.g. GARP)
Internet
7
openModeller, distributed,open architecture
Client(e.g. openModeller Desktop)
SOAP Server
Condor
SOAP Client Layer
Modelling Engine (libopenmodeller)
Modelling Engine (libopenmodeller)
Modelling Engine (libopenmodeller)
Cluster
Modelling Algorithm (e.g. GARP)
Modelling Algorithm (e.g. GARP)
Internet
Modelling Algorithm (e.g. GARP)
8
openModeller, distributed,open architecture
Client(e.g. openModeller Desktop)
SOAP Server
Modelling Engine (MaxEnt)
SOAP Client Layer
Internet
9
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 SOAPLite on client side (console) and
  gSOAP on client side (GUI).
• Protocol not specific to openModeller

10
getLayers()

• Used to determine what environmental layers are
  on the server.

11
getLayers()

• Presented to user as heirachical tree
• Layers have identifiers that could resolve files,
  database urls (WCS in the future)

12
getAlgorithms()

• Used to determine what modelling algorithms are
  on the server.

13
getAlgorithms()

• Presented to user as list
• Users can set parameter values
• Document includes descriptive data to aid user
  decision making

14
createModel()

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

15
createModel()

• Returns a serialised model definition document

16
projectModel()

• Used to render a probaility of occurence map

17
getMapAsUrl()
18
Additional Methods

• ping()
• getProgress()
• getLog()
• getMapAsUrl()
• getMapAsAttachment()

19
Integration With TDWG/OGC

• Automated 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)

20
Acknowledgements
CRIA, Brazil (http//cria.org.br)FAPESP, Brazil
(http//www.fapesp.br)
More Info
http//openmodeller.sf.net