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Software Tools


Zotero is an open source reference management software which manages bibliographic data and related research materials (such as PDFs). On many websites such as library catalogs, PubMed, Google Scholar, Google Books, Amazon.com, Wikipedia, and publisher's websites, Zotero shows an icon when a book, article, or other resource is being viewed. By clicking this icon, the full reference information can be saved to the Zotero library. Zotero can also save a copy of the webpage, or, in the case of scientific articles, a copy of the full text PDF. Users can then add notes, tags, attachments, and their own metadata. Selections of the local reference library data can later be exported as formatted bibliographies. Furthermore, all entries including bibliographic information and user-created rich-text memos of the selected articles can be summarized into an HTML report. Other notable features: web browser integration, online syncing, generation of in-text citations, footnotes and bibliographies, as well as integration with the word processors Microsoft Word, LibreOffice and OpenOffice.org Writer.

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Tags: bibliography,citation,collaboration,social networking,web 2.0 Contributor: GW, MD Cost: Free
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Xtme 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)ÅÇ Xtme has a number of command line options and shortcuts to ease the navigation and editing among the information placeholders. Xtme 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.

Additional Information:
  • Further Documentation: http://geology.usgs.gov/tools/metadata/tools/doc/metadata/xtme.html
  • About the Content Standards for DIgital Geospatial Metadata http://www.fgdc.gov/metadata/csdgm/
    Content for Digital Geospatial Metadata
  • Tags: FGDC,metadata,metadata editor Contributor: Cost: Free
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    XML Spy

    XMLSpy is an advanced XML editor for modeling, editing, transforming, and debugging XML-related technologies. XMLSpy allows developers to create XML-based and Web services applications using technologies such as XML, XML Schema, XSLT, XPath, XQuery, WSDL, and SOAP. XMLSpy is also available as a plug-in for Microsoft Visual Studio and Eclipse.

    Additional Information: Tags: XML Contributor: Cost: Cost-basis
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    xCase is a data modeling and database design tool that is used to create logical and physical data models. xCase can create the actual database from the physical model, and create different physical implementations from a single logical model. xCase can also reverse-engineer existing databases into a model diagram. xCase works with many database management systems (DBMS). Major output from the tool include entity-relationship (ER) diagrams and standard or custom reports on all objects in the design (tables, fields, relationships).

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    Tags: database,models Contributor: ST, RL Cost: Cost-basis
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    WordPress is an open source content management system (CMS). It provides a structured website that enables users to create and edit various types of web content without requiring in depth technical knowledge of web authoring or programming languages.

    Novice users can create web pages and add basic text and graphics to them with only a minimal introduction to the system; they can also take advantage of WordPress plugins, widgets, and themes. WordPress can also be used simply as a blogging tool.

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    While WordPress does not require technical skills to use once it is installed, as a server application the initial implementation of WordPress needs to be performed by a systems administrator with at least intermediate skills in server installation and management. There are also many hosting sites available (http://wordpress.org/hosting/), generally for a fee.
    Ask around your department, lab, or institution, Wordpress instances may already be available to you.

    Resources, guides and help: https://firstsiteguide.com/learn-wordpress/

    Tags: Contributor: SL, MG Cost: Free
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    WinBUGS is software for running Markov Chain Monte Carlo (MCMC) simulations following Bayesian statistical theory. It is one of two software packages created for Bayesian Inference Using Gibbs Sampling, or BUGS. WinBUGS is so named because it runs on windows operating systems; the OpenBUGS software can be used on other operating systems (see OpenBUGS entry).

    Bayesian inference is built on specified probabilities of models and evaluated using MCMC simulation including error components. WinBUGS implements these simulations and "samples" them according to user-defined criteria. WinBUGS can be used as a stand-alone application but can also be integrated with R statistical software using the R2WinBUGS package in R.

    WinBUGS requires thorough knowledge of Bayesian statistics to create and evaluate models appropriately.

    Additional Information:
    Tags: analyze,models,statistics Contributor: EL, SL Cost: Free
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    WEKA is a data mining tool. It is a collection of standard machine learning algorithms organized and presented to the user as a workbench. The algorithms can be applied directly to a dataset from the workbench or called from Java code. New classifiers, filters etc can be added through the GUI.

    WEKA is written in Java and runs on platforms that support Java. It is available under the GNU Public License (GPL).

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    Tags: analyze,computing,data mining Contributor: SA, RO Cost: Free
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    Webex is a proprietary web collaboration and meeting environment. WebEx allows users to host and join web video- and tele-conferences. WebEx requires client-side Java, a browser, and a plugin, but once installed, users can host and join meetings with a browser and no additional software. WebEx web conferencing allows any user to become the "presenter" can share an application or their entire desktop over the web with other meeting participants. The presenter can give mouse control to other users, thereby allowing people to engage interactively in the conference and directly edit documents on another's computer. WebEx is often used for presentations using programs such as PowerPoint in distributed meetings.

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    Tags: collaboration,computing,web 2.0 Contributor: DG, ST Cost: Cost-basis
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    Web Accessible Folder (WAF) Tools

    A collection of Extensible Stylesheet Language Transformations (XSLT) for transforming between various metadata standards and views, and a tool for applying those transforms to metadata records stored in Web Accessible Folders (WAF, https://geo-ide.noaa.gov/wiki/index.php?title=Web_Accessible_Folder). The focus is on translating FGDC metadata to ISO and on translating that ISO into various other standards and views.

    Additional Information:

    People wishing to use their own XSLT transformations can contact information managers at NOAA's Global Earth Observation - Integrated Data Environment (GEO-IDE) Initiative about loading them on the website.

    Tags: FGDC,metadata,standards,XML Contributor: TH, MG Cost: Free
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    VisTrails is an open-source scientific workflow and provenance management system developed at the University of Utah that provides support for data exploration and visualization. Whereas workflows have been traditionally used to automate repetitive tasks, for applications that are exploratory in nature, such as simulations, data analysis and visualization, very little is repeated---change is the norm. As an engineer or scientist generates and evaluates hypotheses about data under study, a series of different, albeit related, workflows are created while a workflow is adjusted in an interactive process. VisTrails was designed to manage these rapidly-evolving workflows.

    Additional Information:
    Tags: provenance,visualization,workflow Contributor: Cost: Free
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