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Software Tools

Ocean Data View (ODV)

Ocean Data View (ODV) is desktop software for analysis and visualization of oceanographic, atmospheric and other geo-referenced profile or time-series data.

Basic features:

  • Input format is basic spreadsheet-styled data tables
  • Users can customize their configurations with high resolution bathymetry, coastlines, and other reference material
  • Data and configuration files are platform-independent and can be exchanged between different systems

ODV is particularly useful for:

  • Plots of properties at selected stations,
  • Cross-sections along cruise tracks, and
  • Color distributions on general isosurfaces

ODV was developed by the Alfred Weneger Institute (http://www.awi.de), under the SeaDataNet program. There are licensing restrictions for uses other than scientific research.

Additional Information:

The NODC data services directory includes other information about this program:

Tags: Contributor: MO, FF Cost: Free
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OAIster is a freely accessible search engine for open access web resources, available from OCLC. OAIster uses the Open Access Initiative Protocol for Metadata Harvesting (OAI-PMH) to harvest records from websites. OAIster contains over 25 million records from all disciplines and subjects contributed by over 1,000 libraries, archives, and repositories. The records harvested by OAIster use Dublin Core (unqualified) metadata format. Repository managers running OAI-compliant repositories can contribute records for open access web resources. OAIster records can be searched separately at the website, and are incorporated into OCLC Worldcat.

Additional Information:
Tags: catalog,data mining,metadata Contributor: PW, RL Cost: Free
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NPS (National Park Service) Metadata Tools & Editor

The NPS Metadata Tools & Editor is a custom software application developed for the National Park Service (NPS) for authoring and editing NPS metadata. It extends the basic functionality of ESRI's ArcCatalog for managing geospatial metadata and also provides a stand-alone version for creating and manipulating non-spatial metadata outside of ArcCatalog. While the tool was not specifically designed for users external to the NPS, the Tools and Editor features powerful metadata editing capabilities that a metadata author is likely to find useful.

Additional Information: Tags: geospatial,GIS,metadata Contributor: Cost: Free
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NodeXL is a free, open-source template for Excel 2007 and 2010 that lets you enter a network edge list, click a button, and see the network graph, all in the Excel window.

You can customize the graph’s appearance; zoom, scale and pan the graph; dynamically filter vertices and edges; alter the graph’s layout; find clusters of related vertices; and calculate graph metrics. Networks can be imported from and exported to a variety of file formats, and built-in connections for getting networks from Twitter, Flickr, YouTube.

Additional Information:
Tags: analyze,graphics,network,visualization Contributor: JF, RO Cost: Free
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ncISO is a package of tools that facilitates the generation of ISO 19115-2 metadata from data in NetCDF (Network common data format).

These data must be included in a Thematic Realtime Environmental Distributed Data Service (THREDDS) data server catalog. ncISO is based on the Unidata Attribute Convention for Data Discovery (http://www.unidata.ucar.edu/software/netcdf-java/formats/DataDiscoveryAt...).

There are currently two tools available, first a command line utility that can be run on your local desktop or workstation, and second a THREDDS server extension library. This utility is also included in the THREDDS Data Server.

Inputs to this tool are THREDDS catalogs.

Outputs from the tool are ISO metadata in XML format.

Additional Information:

Information on NetCDF data format: http://www.unidata.ucar.edu/software/netcdf/

Tags: metadata,standards Contributor: TH, EL Cost: Free
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National Instruments LabVIEW

National Instruments LabVIEW is a sophisticated application for the creation and management of engineering and scientific measurement, test, data collection and control systems. LabVIEW includes a graphical user interface that allows external hardware devices such as mechanical or electronic sensors to be configured and operated using "point-and-click" methods. Networks of sensors and processing devices can be joined together using flowchart-like "wire" connectors. Both physical and virtual (software-based) devices are supported. Complex processes, virtual devices and workflows can be developed using the LabVIEW programming language instead of the GUI interface. In addition to device management, LabView provides an extensive set of on-board analysis libraries that enable data feeds to be aggregated, evaluated and manipulated. Raw and processed data can then be routed to a remote database platform or other repository for storage. LabView also provides numerous plug-ins that enable both live and stored data to be visualized in various types of charts, graphs and tables, and includes a technical reporting module that allows data output to be formatted for print or online distribution.

Additional Information:

LabView has detailed system requirements for each major platform upon which it is supported. Please see the LabView requirements page at: http://www.ni.com/labview/requirements/ for more information.

LabView is a commercial product, but a 30-day trial version is available at: http://www.ni.com/trylabview/

Tags: analyze,GUI,remote sensing,visualization Contributor: KC, JP Cost: Cost-basis
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MySQL Workbench

MySQL Workbench is an open source, visual based tool for MySQL database design, creation and administration. It is separate from, but connects to MySQL, which is database software built on a version of Structured Query Language or SQL (see MySQL tool description in the DataONEpedia).

SQL Development
Create and manage connections to database servers.
Enables the user to configure connection parameters.
Capability to execute SQL queries on the database connections using the built-in SQL Editor.
Data Modeling
Enables you to create models of your database schema graphically.
Forward engineer, or turn diagrams into MySQL databases.
Reverse engineer, or download existing MySQL databases and represent them as diagrams.
Edit Tables, Columns, Indexes, Triggers, Partitioning, Options, Inserts and Privileges, Routines and Views.
Database Administration
Enables you to create and administer server instances.
Manage users and user permissions.
Additional Information:
Tags: database,server Contributor: RO, EL Cost: Free
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MySQL is a relational database system (RDBMS) that runs as a server providing multi-user access to several databases. All major programming languages include libraries to access MySQL. It comes with a command line tool, with many third party graphical user interfaces also available. Although not considered a full enterprise RDBMS like Oracle or PostgreSQL, it supports most RDBMS technologies like foreign keys, triggers, views, indexing, and backup. MySQL is easy to use, sufficient for most environmental data management applications and the choice of many web server hosting companies.

MySQL is included in several third party installation bundles, providing easy installation and configuration for the most popular combinations of programs for web development. E.g. LAMP, WAMP etc. which combine Apache webserver, MySQL and PHP for Linux and Windows respectively.

Additional Information: Tags: data storage,database,server Contributor: Cost: Free
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myExperiment is a collaborative environment where scientists can safely publish their workflows and experiment plans, share them with groups and find those of others. It allows workflows, other digital objects and bundles (called Packs) to be swapped, sorted and searched like photos and videos on the Web. myExperiment makes it easy for the next generation of scientists to contribute to a pool of scientific methods, build communities and form relationships - reducing time-to-experiment, sharing expertise and avoiding reinvention.

Additional Information:
  • De Roure, D., Goble, C. and Stevens, R. (2009) The Design and Realisation of the myExperiment Virtual Research Environment for Social Sharing of Workflows. Future Generation Computer Systems 25, pp. 561-567. doi:10.1016/j.future.2008.06.010
  • Goble, C.A., Bhagat, J., Aleksejevs, S., Cruickshank, D., Michaelides, D., Newman, D., Borkum, M., Bechhofer, S., Roos, M., Li, P., and De Roure, D.: myExperiment: a repository and social network for the sharing of bioinformatics workflows, Nucl. Acids Res., 2010. doi:10.1093/nar/gkq429
  • De Roure, D. and Goble, C. (2009) "Software Design for Empowering Scientists," IEEE Software, vol. 26, no. 1, pp. 88-95, January/February 2009. doi:10.1109/MS.2009.22
Tags: repository,social networking,web 2.0 Contributor: Cost: Free
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MrBayes is a program for doing Bayesian phylogenetic analysis including phylogenetic reconstruction. Bayesian inference of phylogeny is based on the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is often impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov Chain Monte Carlo (MCMC) to approximate the posterior probabilities of trees.

Additional Information:

Huelsenbeck JP, Ronquist F., MRBAYES: Bayesian inference of phylogenetic trees,Bioinformatics. 2001 Aug;17(8):754-5.

Fredrik Ronquist and Andrew R. Deans, Bayesian Phylogenetics and Its Influence on Insect Systematics, Annual Review of Entomology
Vol. 55: 189-206 (Volume publication date January 2010),First published online as a Review in Advance on October 5, 2009,DOI: 10.1146/annurev.ento.54.110807.090529

Tags: Contributor: RK, DG Cost: Free
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