I want to search


We've launched a new website!

You're currently accessing the archived version of the DataONE website. To see our new design and keep up to date with the latest DataONE news, visit our new website at https://dataone.org

Software Tools

GeoNetwork OpenSource

GeoNetwork OpenSource is an open source geospatial data catalog service host, metadata creation and management system, and basic web mapping platform that is in broad use by a number of international organizations in deploying their Spatial Data Infrastructure (SDI). GeoNetwork implements a set of key international geospatial standards, including catalog service (OGC Catalog Services for Web [CSW], z39.50), metadata (FGDC, ISO19139, Dublin Core [for general documents]), and map visualization (OGC Web Map Services [WMS]) standards that allow for integration of GeoNetwork services into national (i.e. NBII, Geospatial OneStop) and international (i.e. GEOSS) geospatial data discovery and access programs.

Additional Information:
Tags: catalog,geospatial,GIS Contributor: Cost: Free
Custom text:
Generic Member Node (GMN)

The DataONE Generic Member Node (GMN) is a complete open-source implementation of a DataONE Member Node (MN). As such, it is a data preservation-oriented repository, and one that manages its content collection through the DataONE MN_Storage API. GMN accepts any metadata format, and provides byte-level persistence of objects.

GMN can be used as a standalone Member Node or it can be used for exposing data that is already available by URL. In the latter case, GMN provides a DataONE compatible interface to existing data and does not store the data. Instead it maintains the associated System Metadata, and other DataONE-specific structures.

GMN can also be used as a software starting point or reference for a 3rd party MN implementation.

If an organization wishes to donate storage space to DataONE, GMN can be set up as a replication target.

GMN is built using the Django Framework and utilizes Apache2 as the web server and PostgresSQL as the underlying RDBMS. Other configurations are possible via adaptation.

Additional Information:
Tags: data storage,Member Node,repository Contributor: Cost: Free
Custom text:

GenePattern is a genomic analysis platform that provides access to more than 150 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

Additional Information:

Michael Reich, Ted Liefeld, Joshua Gould, Jim Lerner, Pablo Tamayo & Jill P Mesirov. GenePattern 2.0, Nature Genetics - 38, 500 - 501 (2006)

Tags: access Contributor: RK, KC Cost: Free
Custom text:
GDAL (Geospatial Data Abstraction Library)

The Geospatial Data Abstraction Library (GDAL) is a C/C++ geospatial data format translation programming library and associated set of utility programs built using the library. Within the GDAL library are two components: the GDAL component which supports the reading/writing/translation of numerous raster formats, and the OGR component which supports reading/writing/translation of numerous vector data formats. The GDAL/OGR library is integrated into a wide variety of Open Source and commercial products as a core data access library for reading and writing geospatial data in the supported data formats. The GDAL/OGR Applicaton Programming Interface (API) has also been implemented in a number of other programming languages for programatic processing of geospatial data, including
• Perl
• Python
• VB6 Bindings (not using SWIG)
• GDAL Bindings into R by Timothy H. Keitt.
• Ruby
• Java
• C# / .Net

Additional Information:
  • OGR Documentation Page: http://www.gdal.org/ogr/index.html
  • Warmerdam, Frank (2008). The Geospatial Data Abstraction Library in Open Source Approaches in Spatial Data Handling. Springer Berlin Heidelberg. pp 87-104
Tags: programming Contributor: Cost: Free
Custom text:

Developed by NASA Global Change Master Directory (GCMD), DocBUILDER is a metadata development tool that can be used to develop collection-level metadata for deposition in the GCMD repository. Any organization or individual can use the tool, although registering an account is a prerequisite. Tool descriptions and other documentation are password protected.

Additional Information:
Tags: Contributor: RD, MO Cost: Free
Custom text:
GBIF IPT (Integrated Publishing Toolkit)

The Integrated Publishing Toolkit (IPT) is a free open source software tool written in Java that is used to publish and share biodiversity datasets through the GBIF network. The IPT can also be configured with either a DataCite or EZID account in order to assign DOIs to datasets transforming it into a data repository. IPT is aimed at users, coders and translators.

If you're only interested in trying out the IPT please request an account on the Demo IPT by sending an email to helpdesk@gbif.org.
The simplest way to begin using the IPT is to request a free account on a trusted data hosting centre allowing you to manage your own datasets and publish them through GBIF.org without the hassle of setting up and maintaining the IPT on your own server.
Otherwise if want to setup your own instance of the IPT the Getting Started Guide is your entry point.

Additional Information:
Tags: biodiversity,data repository,metadata,metadata editor,sampling-event data,species occurrence data Contributor: Cost: Free
Custom text:

Gallery is a web-based image management system characterized as a "photo album organizer." Typical uses are to display collections of photographs on a web page. Index pages allow users to view small "thumbnail" versions of images, with the ability to zoom in to see images. Image upload capabilities and searching are also supported.

Written in the PHP programming language, there are several versions (1,2 and 3) of Gallery available and still undergoing development. They differ slightly in their capabilities and in the type of database used. Gallery 1 uses an integrated file-based database system, Gallery 2 & 3 use an external database (e.g., MySQL).

Additional Information:
Tags: database,image Contributor: JP, CJ Cost: Free
Custom text:
Fusion LiDAR Software

Fusion is a LiDAR viewing and analysis software tool developed by the Silviculture and Forest Models Team, Research Branch of the US Forest Service. Fusion also works with IFSAR and terrain data sets. LIDAR uses a laser sensor comprised of a transmitter and receiver, a geodetic-quality Global Positioning System (GPS) receiver and an Inertial Navigation System (INS) unit. The laser sensor is mounted to the underside of an aircraft. Once airborne, the sensor emits rapid pulses of infrared laser light, which are used to determine ranges to points on the terrain below. For more information: http://forsys.cfr.washington.edu/fusion/fusion_overview.html

Additional Information:

This application is designed for Internet Explorer version 5 and above. If you are using and older version of IE, the application may not open or it may behave in unexpected ways. This application will not function with Mozzilla FireFox and NetScape browsers.

Tags: Contributor: TV, JB Cost: Free
Custom text:
FRAGSTATS: Spatial Pattern Analysis Program for Categorical Maps

FRAGSTATS is a computer software program designed to work with geospatial data to help the user categorize landscape patterns and metrics, and is useful in identifying areas where land use activities have resulted in fragmentation of the landscape. The current release is version 3.3

The program is currently undergoing another major revamping, which will result in the release of version 4.0 sometime in 2011.

Additional Information:

Version 3.3 is a stand-alone program written in Microsoft Visual C++ for use in the Windows Operating environment. It accepts raster images in a variety of formats, including Arc Grid, ASCII, 16 or 32 bit BINARY, ERDAS, and IDRISI image files. However, currently FRAGSTATS does not work with newer versions of ERDAS Imagine files.

Tags: analyze,geospatial,GIS,map Contributor: TV, JB Cost: Free
Custom text:
Forest Sector Carbon Calculator

The Forest Sector Carbon Calculator is a tool to help users learn about how carbon stores in the forest change over time.

The Forest Sector Carbon Calculator integrates a number of kinds of software to gather information from users, process, and then output results. The foundation for the Calculator is a model called LANDCARB that is designed to simulate the dynamics of living and dead pools of carbon in forest stands and landscapes. It also includes a submodel that estimates how harvested carbon is manufactured into forest products, as well as how these are used, and disposed.

This web interface allows users to control scenarios by selecting different regions, integrating past histories of disturbance and management, and choosing alternative futures. Calculations can be done for a single stand or for an entire landscape. Reports and time trend graphs on stores in the forest, in wood products (including bioenergy), and disposal can be generated.

Additional Information:
Tags: analyze,discover,models,niche modeling,visualization Contributor: TV, CS Cost: Free
Custom text: