Analytical and Modeling Tools

The analysis and modeling of data is one of the core activities of ecological science. While a variety of off-the-shelf software packages exist for analysis and modeling (e.g., SAS, Matlab, Arc Info), there are also several extremely useful open-source tools available.
Kepler - an analytical system that allows users to construct scientific workflows that model the way data flows among discrete analytical components. The Kepler system provides support for a wide variety of analytical components, and makes it easy to incorporate R and Matlab scripts in workflows.
R - an analytical system that allows users to conduct a wide variety of statistical analyses. R is a modular scripting system with an incredibly wide variety of user-contributed libraries for popular forms of statistical analysis.

Metadata Specifications

Metadata, or "data that describes data", is essential for use in analysis and modeling of ecological data. Commonly-used specifications include:
EML - a metadata specification developed by the ecology discipline and for the ecology discipline, based on prior work done by the Ecological Society of America and associated efforts. EML is implemented as an XML schema that can be used to document ecological data.
NBII - The NBII biological metadata standard has been developed as a "biological data profile" of the Federal Geographic Data Committee's (FGDC) Content Standard for Digital Geospatial Metadata (CSDGM)
FGDC - the Content Standard for Digital Geospatial Metadata (CSDGM) provides a common set of terminology and definitions for the documentation of digital geospatial data.

Metadata Editors

Metadata collection can be facilitated by use of an editor or metadata-entry application, such as the following:
Morpho - an easy-to-use, cross-platform data management application allowing ecologists to create, access and manipulate EML metadata and data, and query, view and retrieve public ecological data.
MetaMaker - NBII MetaMaker is a metadata/data entry program for MS Windows, and is based on and in full compliance with the FGDC CSDGM and the Draft Content Standard for NBII Metadata.

Data Repositories

Tight integration of metadata and data is key to quick and efficient reporting and analysis tasks -- a solid data storage system, which is flexible and broadly available, is valuable to all organizations:
Metacat - a flexible metadata database that utilizes XML as a common syntax for representing the large number of metadata content standards relevant to ecology. Thus, Metacat is a generic XML database that allows storage, query, and retrieval of arbitrary XML documents without prior knowledge of the XML schema.
SRB - The SDSC Storage Resource Broker (SRB) is a client-server middleware that provides a uniform interface for connecting to heterogeneous data resources over a network and accessing replicated data sets. SRB, in conjunction with the Metadata Catalog (MCAT), provides a way to access data sets and resources based on their attributes rather than their names or physical locations.
Ecogrid - Providing the Grid infrastructure for seamless access and manipulation of ecology data and tools. EcoGrid is an infrastructure that combines features of a Data Grid for ecological data and a Compute Grid for analysis and modeling services.


Without data, our models and hypotheses are useless. Thanks to broad networks, data are available with the click of a mouse:
Vegbank - the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification.
CLIMDB - a centralized server to provide open access to long-term meteorological records from a collection of research sites.
HerpNET - a collaborative effort by institutions in the United States, Canada and Mexico to establish a network between databases of herpetological collections.