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Software Tools

Scientific Python (SciPy)

Scientific Python (SciPy) is an interactive programming environment for mathematics, science and engineering based on the open source Python programming language. SciPy builds on NumPy, a Python library that provides convenient and fast N-dimensional array manipulation, and includes many user-friendly and efficient routines for numerical integration and optimization, data analysis, and plotting. Tutorials and recipes are provided for common data analysis scenarios, and support is provided by an active community of scientific end-users.

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SAS Enterprise Miner

SAS Enterprise Miner streamlines the data mining process to create predictive and descriptive models based on analysis of large amounts of data. Data can be accessed from local files or from remote database connections. SAS data mining software uses a point-and-click interactive interface to create workflows and analysis diagrams, and then execute them. SAS Miner can transform and manipulate data using filters and statistical analyses to extract desired data from large datasets.

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Tags: analyze,data mining,models,statistics Contributor: FF, EL Cost: Cost-basis
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SAS is an integrated system of software that enables everything from data access across multiple sources to complex manipulations of data files to performance of sophisticated statistical analyses and data visualizations. Three of SAS' most popular software products that are commonly used by ecologists are Base SAS, SAS/STAT, and SAS/GRAPH. SAS is available for Windows and UNIX platforms. GUIs make SAS accessible to novice users and the command-line interface facilitates development of programs for complex data processing.

Additional Information:
  • Khattree, Ravindra and Dayanand N. Naik. 2000. Multivariate Data Reduction and Discrimination with SAS Software. Cary, NC: SAS Institute Inc. 978-1-58025-357-4
  • Littell, Ramon C., George A. Mi lliken, Walter W. Stroup, Russell D. Wolfinger, and Oliver Schabenberger. 2006.SAS for Mixed Models, Second Edition. Cary, NC: SAS Institute Inc. ISBN: 978-1-59047-500-3
  • SAS Essentials: A Guide to Mastering SAS for Research. 2010. Elliott, Alan C. and Wayne A. Woodward. San Francisco: John Wiley and Sons, Inc. ISBN: 978-0470461297
  • Delwiche, Lora D. and Susan J. Slaughter. 2008. The Little SAS Book: A Primer (Fourth Edition). Cary, NC: Sas Institute Inc. ISBN: 978-1-59994-725-9
  • Burlew, Michele. 2009. Combining and Modifying SAS Data Sets: Examples, Second Edition. Cary, NC: SAS Institute Inc. ISBN: 978-1-59047-920-9
Tags: data mining,graphics,statistics Contributor: Cost: Cost-basis
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S-PLUS is a commercial implementation of the S statistical programming language with a publication-quality graphics package and a matrix-based programming language. It provides the ability to analyze gigabyte class data sets on the desktop, and a package system for deployment of analytics.

The R programming language is an open-source implementation of the S statistical programming language.

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RightField is an open-source tool for adding ontology term selection to Excel spreadsheets. RightField is used by a 'Template Creator' to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used.

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Tags: spreadsheet Contributor: Cost: Free
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Refworks is an easy-to-use web-based product that allows you to import references. RefWorks is a subscription-based service available in many Higher Ed institutions. For subscribers, you can import references from your institutions' online library catalog and many electronic databases to which the institution subscribes. It is designed to help researchers easily gather, manage, store and share all types of information, as well as generate citations and bibliographies.

More specifically, RefWorks enables you to...

  • Download citations from databases and put them into a personal RefWorks research database
  • Format bibliographies and citations automatically in over 400 styles including APA, MLA, etc.
  • Create a bibliography of citations in a Word document using a RefWorks "as-you-write-it" add-in.
  • Access your RefWorks account from any computer, anywhere
  • Create a database and share it with colleagues around the world
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    Tags: bibliography,catalog,citation,metadata Contributor: SL, JP Cost: Cost-basis
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    Rational Rose

    Rational Rose is a software development environment for using model descriptions and pattern languages to drive code development. Rational Rose is an IBM product. The emphasis of the "rational" development environment is to design major software engineering components at an abstract modeling level, initially unhindered by the challenges of implementing components and relationships as code. Common technologies driving rational development are APIs (Application Programming Interfaces) to encapsulate interfaces from implementation, UML (Unified Modeling Language) to express abstract entities and their relations, and IDEs (Integrated Development Environments) to coordinate the various modeling and coding artifacts.

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    Tags: models,programming Contributor: DG, ST Cost: Cost-basis
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    RAMADDA (Repository for Archiving, Managing and Accessing Diverse DAta)

    RAMADDA is a web-based application framework that provides a broad suite of services for content and data management, publishing and collaboration. RAMADDA brings together a number of concepts and technologies to provide an easy to use but powerful system for publishing, organizing, discovering. and accessing data and other holdings.
    RAMADDA Is a freely available web application that runs on your own server. Java is necessary for operation.

    RAMADDA provides the following features:

    • Data file ingest, organization, meta-data creation and access control
    • Search and browse capabilities
    • Catalog and RSS feeds
    • Data services including OpenDAP, subsetting and point data access
    • Wiki facilities
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    Tags: access,discover,metadata Contributor: Cost: Free
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    R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. R is highly extensible and has many user-submitted packages for specific functions or specific areas of study such as bioinformatics, ecological models, population dynamics, analysis of spatial data, and phylogenetis. Packages can be browsed by CRAN Task Views. These views may be of interest: Analysis of Ecological and Environmental Data, Statistical Genetics, Phylogenetics, Especially Comparative Methods, and Analysis of Spatial Data. There are several graphical user interface (GUI) packages that can simplify the use of R, including Tinn-R, R Commander, and SciViews.

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    Quantum GIS (QGIS)

    Quantum GIS (QGIS) is an open source Geographic Information System (GIS) that implements a large number of geospatial data access, visualization, processing, and analysis functions. It can access vector data stored in a wide variety of formats, including file-based (e.g. ESRI Shape Files, KML, GML), geodatabases (e.g. PostgreSQL/PostGIs, ODBC, ESRI Personal GeoDatabase, SQLlite), and network protocols (OPeNDAP, GeoJSON); raster data in one of over 40 formats supported by the underlying GDAL raster library (including NetCDF, HDF5, GeoTIFF, GRIB, and JPEG-2000); and Open Geospatial Consortium visualization and data access services (Web Map and Web Feature Services [WMS and WFS, respectively]). Depending upon the host system configuration, QGIS can also act as an alternative Graphical User Interface for the large collection of GRASS GIS geospatial processing functions. QGIS includes a "plug-in" architecture in which extensions to the core functionality of the application may be developed and used, with current plug-ins including support for GPS integration, interaction with the OpenStreetMap data servers, and data transformation tools.

    Additional Information:
  • OSGeo web site for QGIS: http://www.osgeo.org/qgis
  • Cagnacci and Urbano (2008). Managing wildlife: A spatial information system for GPS collars data. Environmental Modelling & Software 23(7): 957-959
  • Tags: geospatial,GIS,map Contributor: Cost: Free
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