ModeleR: An enviromental model repository as knowledge base for experts

In this paper, we present the development of ModeleR, a repository of models accessible from the web, which enables the user to design, document, manage, and execute environmental models. The technique and features offered can be applied to any scientific context. Based on the development of its ontology, a metadata system has been established to document the modeling process. The set of models managed from ModeleR reflects the knowledge base of the experts of the system, allowing other experts to reuse, replicate, and delve deeper into the existing models in the repository. Different levels of integration have been included, from the conceptual description of the model to the process needed to execute a model from a remote server, acting as an execution engine through the use of workflow managers. In this paper, we present the problems encountered as well as the solutions reached on developing a prototype of ModeleR set up for ecosystem research and an environmental monitoring lab.

[1]  Inigo San Gil,et al.  Metadata Activities in Biology , 2010 .

[2]  Bertram Ludäscher,et al.  Kepler: an extensible system for design and execution of scientific workflows , 2004 .

[3]  Christopher R. Johnson,et al.  The SCIRun Computational Steering Software System , 1997, SciTools.

[4]  M. Waldrop,et al.  Science 2.0. , 2008, Scientific American.

[5]  Matthew S. Shields,et al.  Triana: a graphical Web service composition and execution toolkit Web Services , 2004 .

[6]  Daniel Crawl,et al.  Workflows and extensions to the Kepler scientific workflow system to support environmental sensor data access and analysis , 2010, Ecol. Informatics.

[7]  Marija D. Ilic,et al.  Interactive object-oriented simulation of interconnected power systems using SIMULINK , 2001, IEEE Trans. Educ..

[8]  David Yehling Allen Using the Dublin Core with CORC to Catalog Digital Images of Maps , 2001 .

[9]  P. McCartney,et al.  Using XML-encoded Metadata as a Basis for Advanced Information Systems for Ecological Research , 2010 .

[10]  Matthew Jones,et al.  Maximizing the Value of Ecological Data with Structured Metadata: An Introduction to Ecological Metadata Language (EML) and Principles for Metadata Creation , 2005 .

[11]  James P. Ignizio An introduction to expert systems : the development and implementation of rule-based expert systems , 1991 .

[12]  Matthew R. Pocock,et al.  Taverna: a tool for the composition and enactment of bioinformatics workflows , 2004, Bioinform..

[13]  N. DiGirolamo,et al.  MODIS snow-cover products , 2002 .

[14]  Linda Cantara METS: The Metadata Encoding and Transmission Standard , 2005 .

[15]  Matthew B. Jones,et al.  Metacat: a schema-independent XML database system , 2001, Proceedings Thirteenth International Conference on Scientific and Statistical Database Management. SSDBM 2001.

[16]  Edward A. Lee,et al.  Scientific workflow management and the Kepler system , 2006, Concurr. Comput. Pract. Exp..

[17]  Remco M. Dijkman,et al.  APROMORE: An advanced process model repository , 2011, Expert Syst. Appl..

[18]  John W. Hearne,et al.  Reducing model complexity via output sensitivity , 2007 .

[19]  John A. Kunze,et al.  Dublin Core Metadata for Resource Discovery , 1998, RFC.

[20]  V. J. Varcoe A note on the computer simulation of crop growth in agricultural land evaluation. , 1990 .

[21]  Heeseok Lee,et al.  Document-based workflow modeling: a case-based reasoning approach , 2002, Expert Syst. Appl..

[22]  Nicholas J. Higham,et al.  Matlab guide , 2000 .

[23]  Joachim Benz,et al.  ECOBAS — modelling and documentation , 2001 .

[24]  Elizabeth H. Dow Encoded Archival Description as a Halfway Technology , 2009 .

[25]  Ian J. Taylor,et al.  Triana: a graphical Web service composition and execution toolkit , 2004, Proceedings. IEEE International Conference on Web Services, 2004..

[26]  Andrea Emilio Rizzoli,et al.  Model and data integration and re-use in environmental decision support systems , 1998, Decis. Support Syst..

[27]  William K. Michener,et al.  NONGEOSPATIAL METADATA FOR THE ECOLOGICAL SCIENCES , 1997 .

[28]  Ann Hanlon,et al.  Using the Dublin Core to Document Digital Art , 2001 .

[29]  John R. Yates,et al.  CEBS object model for systems biology data, SysBio-OM , 2004, Bioinform..

[30]  J. Hobbie,et al.  Scientific Accomplishments of the Long Term Ecological Research Program: An Introduction , 2003 .

[31]  Peter F. Patel-Schneider,et al.  OWL 2 Web Ontology Language New Features and Rationale , 2009 .

[32]  Tim O'Reilly,et al.  What is Web 2.0: Design Patterns and Business Models for the Next Generation of Software , 2007 .

[33]  Jianwu Wang,et al.  Kepler + Hadoop: a general architecture facilitating data-intensive applications in scientific workflow systems , 2009, WORKS '09.

[34]  Morgan V. Cundiff An introduction to the Metadata Encoding and Transmission Standard (METS) , 2004 .