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Software Tools

uDIG (User-friendly Desktop Internet GIS)

uDIG (User-friendly Desktop Internet GIS) is an Open Source GIS framework and application for desktop GIS data access, editing, and viewing. uDIG is based upon the Eclipse Rich Client (RCP) Java framework and is extensible through the addition of plugins developed using the RCP framework. In its base configuration it supports a variety of data access methods, including file-based raster and vector data, geodatabases, and Open Geospatial Consortium services (Web Map and Web Feature Services [WMS and WFS respetively]). Plug-ins have already been developed for geospatial processing and analysis, enhanced cartographic capabilities, OGC Web Processing Service interaction, and data creation.

Additional Information:

Foerster, T. and Schäffer, B. 2007. A client for distributed geo-processing on the web. In Proceedings of the 7th international Conference on Web and Wireless Geographical information Systems (Cardiff, UK, November 28 - 29, 2007). J. M. Ware and G. E. Taylor, Eds. Lecture Notes In Computer Science. Springer-Verlag, Berlin, Heidelberg, 252-263.

Tags: geospatial,GIS,web services Contributor: Cost: Free
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UCINET is a comprehensive package for the analysis of social network data as well as other 1-mode and 2-mode data. Social network analysis methods include centrality measures, subgroup identification, role analysis, elementary graph theory, and permutation-based statistical analysis. In addition, the package has strong matrix analysis routines, such as matrix algebra and multivariate statistics.

Integrated with UCINET is the NetDraw program for drawing diagrams of social networks.

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Tags: access,analyze,social networking,visualization,web 2.0 Contributor: FF, JB Cost: Cost-basis
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Triana is an open source problem solving environment that combines an intuitive visual interface with powerful data analysis tools. It can be used for a range of tasks, such as signal, text and image processing, and Triana includes a large library of pre-written analysis tools and the ability for users to integrate their own tools. Recently a custom writer was attached to the Triana GUI allowing Triana to generate Pegasus/Condor input files for the GriPhyN project.

Additional Information:
  • The Triana Workflow Environment: Architecture and Applications. I. Taylor, M. Shields, I. Wang, and A. Harrison. In I. Taylor, E. Deelman, D. Gannon, and M. Shields, editors, Workflows for e-Science, pages 320-339. Springer, New York, Secaucus, NJ, USA, 2007.
  • Programming Scientific and Distributed Workflow with Triana Services. David Churches, Gabor Gombas, Andrew Harrison, Jason Maassen, Craig Robinson, Matthew Shields, Ian Taylor and Ian Wang. In Concurrency and Computation: Practice and Experience (Special Issue: Workflow in Grid Systems), 18(10):1021-1037, 2006.
  • Visual Grid Workflow in Triana. I. Taylor, M. Shields, I. Wang, and A. Harrison. In Journal of Grid Computing, 3(3-4):153-169, September 2005.
  • Related tools: GriPhyN project, Pegasus
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    TMI-Orion QLEVER

    TMI-Orion is a manufacturer of data sensors and data loggers. They have custom software called QLEVER to configure, test, record data and perform basic statistics on the data streams resulting from the sensors. The software can manage the sensors (in some cases remotely), and evaluate sensor battery life and technical performance.

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    Tags: analyze,real-time,remote sensing,statistics Contributor: EL, CS Cost: Cost-basis
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    Tkme is a program for creating and modifying formal metadata that conforms to the Content Standards for Digital Geospatial Metadata devised by the Federal Geographic Data Committee (FGDC). Tkme is related to its progenitor, Xtme which ran exclusively on Unix systems. Tkme is closely allied with mp, a compiler for formal metadata, whose purpose is to verify that the syntactical structure of a file containing formal metadata conforms to the FGDC standard, and to re-express the metadata in various useful formats. The editor is intended to simplify the process of creating metadata that conform to the standard.

    Tkme is an improved version of Xtme, built with Tcl/Tk instead of direct calls to the X Window System. This enables Tkme to run on Microsoft Windows as well as Unix systems.

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    Tags: FGDC,metadata,metadata editor Contributor: Cost: Free
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    Tika java class library available through the Apache group. It supports media type detection based on file type signatures, metadata extraction and text parsing and extraction.

    Supported Document Formats:

  • HyperText Markup Language
  • XML and derived formats
  • Microsoft Office document formats
  • OpenDocument Format
  • Apple iWorks Formats
  • Portable Document Format
  • Electronic Publication Format
  • Rich Text Format
  • Compression and packaging formats
  • Text formats
  • Audio formats
  • Image formats
  • Video formats
  • Java class files and archives
  • Mail formats
  • The DWG (AutoCAD) format
  • Font formats
  • Scientific formats
  • The Tika application can be run in either command line mode or as a graphical user interface (GUI) mode. Tika is written in Java and the class library can be used in directly in other programs where needed.

    Those with advanced programming skills can extend the Tikal to meet specific project or analysis needs not covered by the basic release. It is an open source project at the Apache Software Foundation and available under the Apache License version 2.0 (ALv2).

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    Tags: analyze,computing,metadata,programming Contributor: SA, RO Cost: Free
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    Thematic Realtime Environmental Distributed Data Services (THREDDS)

    The THREDDS Data Server (TDS) is a web server that provides metadata and data access for scientific datasets, using OPeNDAP, OGC WMS and WCS, HTTP, and other remote data access protocols. It's features include:

    • THREDDS Dataset Inventory Catalogs are used to provide virtual directories of available data and their associated metadata. These catalogs can be generated dynamically or statically.
    • The Netcdf-Java/CDM library reads NetCDF, OpenDAP, and HDF5 datasets, as well as other binary formats such as GRIB and NEXRAD into a Common Data Model (CDM), essentially an (extended) netCDF view of the data. Datasets that can be read through the Netcdf-Java library are called CDM datasets.
    • TDS can use the NetCDF Markup Language (NcML) to modify and create virtual aggregations of CDM datasets.
    • An integrated server provides OPeNDAP access to any CDM dataset. OPeNDAP is a widely used, subsetting data access method extending the HTTP protocol.
    • An integrated server provides bulk file access through the HTTP protocol.
    • An integrated server provides data access through the OpenGIS Consortium (OGC) Web Coverage Service (WCS) protocol, for any "gridded" dataset whose coordinate system information is complete.
    • An integrated server provides data access through the OpenGIS Consortium (OGC) Web Map Service (WMS) protocol, for any "gridded" dataset whose coordinate system information is complete. This software was developed by Jon Blower (University of Reading (UK) E-Science Center) as part of the ESSC Web Map Service for environmental data (aka Godiva2).
    • The integrated ncISO server provides automated metadata analysis and ISO metadata generation.
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    Tags: content management system,data integration,visualization Contributor: TH, RD Cost: Free
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    The Predictive Ecosystem Analyzer (PEcAn)

    The Predictive Ecosystem Analyzer (PEcAn) is an integrated ecological bioinformatics toolbox and data assimilation system that synthesizes information contained in ecological models, data, and expert knowledge. This is done using modern statistical methods and state-of-the art ecosystem models. PEcAn has a web interface that enables users to run ecosystem models, as well as a suite of R packages that can be used for model-data fusion and more sophisticated analysis.

    Additional Information:

    PEcAn can be used to run ecosystem models through a web-based user interface, while advanced analyses can be performed using its suite of R packages. New models can be linked to PEcAn through the creation of model-specific wrapper functions that convert translate to and from the standard formats used by PEcAn. Although PEcAn is currently coupled to three diverse ecosystem models, it can be coupled to a broad class of simulation models. Integrating a new model requires writing a wrapper in R to convert inputs and outputs to and from the standards used by PEcAn, and registering the model and computer in the database.
    PEcAn source repository is hosted at GitHub: (http://github.com/PecanProject/pecan). See the Wiki (http:// github.com/PecanProject/pecan ) for more information.
    LeBauer, D.S., D. Wang, K. Richter, C. Davidson, & M.C. Dietze. (2013). Facilitating feedbacks between field measurements and ecosystem models. Ecological Monographs. doi:10.1890/12-0137.1
    Wang, D, D.S. LeBauer, and M.C. Dietze (2013) Predicting yields of short-rotation hybrid poplar (Populus spp.) for the contiguous US through model-data synthesis. Ecological Applications doi:10.1890/12-0854.1
    Dietze, M.C., D.S LeBauer, R. Kooper (2013) On improving the communication between models and data. Plant, Cell, & Environment doi:10.1111/pce.12043

    Tags: computing,data mining,database,models,statistics,workflow Contributor: David LeBauer Cost: Free
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    TFRI EML Metadata Analysis Tools

    The Taiwan Forestry Research Institute has produced a set of web-accessible tools that use Ecological Metadata Language (EML) documents to produce maps and statistical products. They are available at: http://metacat.tfri.gov.tw/tfri/.

    One tool creates an "R" statistical language program from an EML document that can then be edited online . Another produces a Google Map displaying locations from the metadata document. A final module ingests an EML document and the associated data and performs quality control checks and simple analyses using a graphical user interface.

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    Tags: EML,map,metadata Contributor: JP, RD Cost: Free
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    TemaTres is an open-source, web-based thesaurus management package. Features include a simple, functional user interface for editing and browsing keywords, sophisticated search capabilities, and the ability to import or export all or part of the thesaurus in a number of standardized forms. TemaTres features a rich set of web services that provide searching and retrieval capabilities for external programs. As a result a number of tools such as "Visual Vocabulary," "ThesaurusWebPublishers" and "TemaTres View" use TemaTres as their backend. There are also capabilities for linking vocabularies in different languages to facilitate the creation of multilingual controlled vocabularies.

    (TemaTres is developed in Argentina, and consequently not all documentation is available in English.)

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    Tags: metadata Contributor: JP, MO Cost: Free
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