Informatics Software & Tools

NCEAS Informatics software products and tools assist scientists in the creation, management, access, and analysis of ecological and environmental data. All the software tools that NCEAS has developed are free for download, typically run on several popular computing platforms, and utilize best-of-class open source software frameworks when appropriate.
 

Analysis and Modeling Tools

Kepler
A reliable, open-source scientific workflow system that enables scientists to design workflows and execute them efficiently. By using a workflow system, researchers can mix together analysis and modeling steps that use a wide variety of computing engines such as R, Matlab, and python.  Kepler facilitates access to a broad range of ecologically relevant data that are housed in the KNB (Knowledge Network for Biocomplexity), while also providing a basis for sharing analyses through a growing library of executable components and workflows. Kepler also provides a demonstration of fully integrated access to sensor networks with the ability to include sensor data in workflows, monitor, inspect, and control sensor networks, and simulate the design of new sensor networks.

DataONE R Client
Providing seamless access from within the R system for statistical analysis to data and metadata held in the DataONE Federation of data repositories. Using the ‘dataone’ library, scientists read data from any DataONE Member repository using its globally unique identifier, making it accessible within R scripts in a way that is portable across computers. Derived data can also be documented and uploaded to the KNB and other DataONE repositories that support data upload.
 

Metadata and Data Management

Morpho 
Enables users to create and manage EML metadata and to share those metadata, and their associated data, with others. It provides an easy-to-use, cross-platform application for accessing and manipulating metadata and data both locally and on the network through powerful connections with Metacat.

Metacat Data Registry 
A web-based form for uploading data sets to Metacat servers such as the KNB repository. This lightweight mechanism for uploading a data set allows researchers to quick share data while still being able to return later to provide more detailed metadata using a tool such as Morpho.
 

Data Repositories

Metacat
A flexible data and metadata repository that can store and version both data and its associated metadata using a wide variety of standards. Metacat has specialized features suitable for guaranteeing local autonomy and access control, while also affording the possibility of broad-scale replication and information sharing as a Member Node in the DataONE network. Metacat servers are used as the basis of the KNB and DataONE networks, as well as many other repositories around the world (PISCO, GulfWatch Alaska, Taiwan Ecological Research Network, and others).

 

Metadata Specifications

Ecological Metadata Language (EML)
A metadata specification for describing tabular (relational) data sets that are common in ecology and earth and environmental science. EML can be used in a modular and extensible manner to document ecological data, including a description of the purpose and contents of a data set, methods used to collect it, people responsible for the data, and details of how to interpret data tables properly.

The Federal Geographic Data Committee (FGDC) Biological Data Profile
A specific profile developed specifically for the FGDC Content Standard for Digital Geospatial Metadata to increase its utility for documenting biological resources data and information.

OBOE (Extensible Observation Ontology)
A semantic model designed to accurately describe observational data in sufficient detail to enable logic-based machine reasoning to help scientists with common research tasks such as finding and merging data sets.
 

Online Databases

KNB Data Repository
Supports the Knowledge Network for Biocomplexity (KNB), a national network that facilitates ecological and environmental research.

NCEAS Data Repository
Information about research data sets collected and collated as part of the NCEAS Working Groups. It is concurrently available through the KNB Data Repository.

GulfWatch Alaska
Repository of data sets from 25 years of research following the Exxon Valdez oil spill in Prince William Sound, Alaska.

Vegbank
The vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification.

Paleobiology Database
Fossil information that includes 52,000 collection records and 511,889 taxonomic occurrences from 13,962 published references.

Interaction Web Database
Data concerning ecological interactions, particularly pollination/pollinator relationships.

Global Population Dynamics Database
An extensive collection of time series data from plant and animal populations.

UC Natural Reserve System Data Registry
The primary source for comprehensive information about scientific and research data sets collected within or under the auspices of the University of California's Natural Reserve System (NRS).

OBFS Data Registry (Organization of Biological Field Stations)
The primary source for comprehensive information about scientific and research data sets collected within or under the auspices of the Organization of Biological Field Stations.

PARC Data Repository (Palmyral Atoll Research Consortium)
Information about the research data sets collected and collated as part of PARC funded activities.

SANParks Data Repository (South African National Park)
The primary source for comprehensive information about scientific and research data sets collected throughout the South African National Park System.