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Software Tools

Spotfire Miner

Spotfire Miner is software for data mining of large datasets. It is sold commerically by TIBCO.

Users can connect to remote or local datasets, apply statistical and methodological filters, clean and transform the data, and finally apply a model to produce the desired mined data. Statistical models include clustering, regression analysis, and principal components analysis. Models based on historical data can then be used to predict future results based on newly mined data.

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Tags: analyze,data mining,models,statistics Contributor: EL, MD Cost: Cost-basis
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Spotfire is a data analysis and visualization tool. It allows users to perform ad-hoc analysis and build custom analytic applications. It supports data imports from spreadsheets and relational databases, as well as real-time and event-driven data. Besides visualization, Spotfire also incorporates statistics functions.

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Tags: analyze,visualization Contributor: JF, GW Cost: Cost-basis
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Specify 6

Specify 6 is a metadata management and collections holdings system that allows you to track specimen and tissue transactions. It manages specimen data such as descriptions of collecting locations, participants and determination histories as well as information about collections transactions such as loans, exchanges, accessions and gifts.

Specify 6 supports georeferencing with GEOLocate, label and report printing, and importing and exporting. You can manage all institutional collections within a single database for simplified administration.

Specify comes in two versions for each desktop operating system. The full version of Specify 6 requires the installation of MySQL database manager and the Java Runtime Environment (JRE). A lighter version of Specify 6, Specify EZDB does not require MySQL installation.

Specify also has a off-line spreadsheet version: Specify Mobile WorkBench. Specify Mobile WorkBench allows scientists to enter data off-line while in the field and then upload to your online Specify database.

Additional Information:

http://specifysoftware.org/content/user-list lists Biological Collections Utilizing Specify Software.

Tags: biodiversity,metadata,metadata editor Contributor: SL, RD Cost: Free
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SpatiaLite is an extension to the SQLite database that enables it to support spatial data.

SpatiaLite is conformant to OpenGIS specifications. It has the following features:

  • supports standard WKT and WKB formats
  • implements SQL spatial functions such as AsText(), GeomFromText(), Area(), PointN() and alike
  • the complete set of OpenGis functions is supported via GEOS, this comprehending sophisticated spatial analysis functions such as Overlaps(), Touches(), Union(), Buffer() ..
  • supports full Spatial metadata along the OpenGis specifications
  • supports importing and exporting from / to shapefiles
  • supports coordinate reprojection via PROJ.4 and EPSG geodetic parameters dataset
  • supports locale charsets via GNU libiconv
  • implements a true Spatial Index based on the SQLite's RTree extension
  • the VirtualShape extension enables SQLite to access shapefiles as VIRTUAL TABLEs
Additional Information:
Tags: analyze,database,geospatial,GIS Contributor: SA, TB Cost: Free
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Skype is VOIP and instant messaging software that allows voice and chat communication between computers and phone systems via the internet. Direct computer to computer via the internet is free of charge, and computer to phone connections via the internet have a relatively small fee. Additional features include video conferencing and file transfer. Acquired by Microsoft in May 2011.

Additional Information:

Basic software installation and computer to computer calling is free. Additional features incur a charge.

Tags: collaboration,communication,network Contributor: RS, JB Cost: Free
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Simulink is an add-on package for MATLAB that supports simulation and model-based design using a graphical block-programming scheme. An interactive graphical editor is provided for building models and simulations based on an extensive library of customizable program blocks and custom code. A Model Explorer application supports inspection and editing of models, signals, parameters and generated code. Simulink provides full access to the MATLAB environment for analyzing and visualizing results, customizing the modeling environment, and defining signal, parameter, and test data.

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Tags: Contributor: Cost: Cost-basis
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SigmaPlot is a commercial software package primarily used for data analysis and publication-quality visualization. Data can be input directly into a table or imported from basic ascii or Microsoft Excel files. Data summarization (e.g., mean, sum) and analysis tools (e.g., parametric and non-parametric statistics, regression, and correlation) operate on the data at a click of the mouse. Graphs or charts in 2-D or 3-D (e.g., line, bar, and pie charts, histograms, heat maps, surfaces) are created via a wizard. Batches of files can be analyzed and graphed automatically. SigmaPlot can also create default or user-defined reports. Specialized functionality of SigmaPlot includes instrument calibration, medical test analysis, and molecular biology tools.

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Tags: graphics,statistics,visualization Contributor: Cost: Cost-basis
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SEEK for Science

The SEEK platform is a web-based resource for sharing heterogeneous scientific research datasets,models or simulations, processes and research outcomes. It preserves associations between them, along with information about the people and organisations involved. Underpinning SEEK is the ISA infrastructure, a standard format for describing how individual experiments are aggregated into wider studies and investigations. Within SEEK, ISA has been extended and is configurable to allow the structure to be used outside of Biology. SEEK is incorporating semantic technology allowing sophisticated queries over the data, yet without getting in the way of your users.

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Tags: collaboration Contributor: Cost: Free
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Scratchpads is a social networking application for biodiversity research. It can by used by researchers to manage, share and publish taxonomic data online. The software has tools for managing:

  • phylogenies
  • classifications
  • bibliographies
  • documents
  • images
  • spreadsheets
  • specimen records
  • maps

Records that are added to a Scratchpad are classified and grouped around a taxonomy. This taxonomy can be supplied by the users or imported from the Encyclopedia of Life. The Scratchpads can link to databases including GenBank, Morphbank, GBIF, Wikipedia, etc.

It provides social networking features, image uploading, free-form page creation, a template for species description (summary data), taxonomic hierarchy editing, importing of images from Flickr and Google Images, a grid-editor for tabular data, mapping functionality, bibliographic data management, and sharing of data with Encyclopedia of Life (http://www.eol.org).

One module allows users to generate publishable manuscripts for taxonomic description or revision in the Zookeys journal. Hosting can be provided by the ViBRANT project or you can host your site yourself. In addition to taxon-based research groups, it has been used by scientific societies and journals to establish a web-presence.

Scratchpads is built using the Drupal content management system.

Additional Information:
Tags: Contributor: CS, EL Cost: Free
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Scientific Python Development Environment (SPYDER)

SPYDER is a free software environment for visualization, numerical calculation, and data analysis. It provides a graphical development environment for the Python programming language and leverages many scientific and engineering packages including Matplotlib, NumPy and others. It is available on Windows, Mac OS X, and GNU/Linux.

Additional Information:
Tags: analyze,statistics,visualization Contributor: CJ, GW Cost: Free
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