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Open Source Software: Science Specific Tools

Data Mining

Data mining essentiially is sorting through large amounts of data to parse out the relevant information. Originally this process of analysis was exclusively under the purvey of business management or information managers.  More recently, science disciplines have turned to  Data mining as a tool to grasp meaning from the large amounts of data produced by current e-science initiatives.

  • Data Mining Tools
    A list of data mining tools are available here.
  • KNIME
    Modular data platform allows you to create visual representation of data flows. Created by the Chair for Bioinformatics and Information Mining - University of Konstanz Germany. Free and adaptable.
  • RapidMiner
    Free and adaptable data mining tool. Select either the "community edition" to use for free or the "developer's edition" to have access to the code.
  • WEKA
    Data mining software in Java. This program does linear regressions, plotting and data visualizations as well. Has an active forum.
  • TOKO
    Open source software for text analysis.
  • G3DATA
    This application is able to extract data from graphs.

Visualization Tools

These tools are for Data Visualization.  Data Visualization is the process of graphicaly presenting your data.  Some simple examples of data visualization are pie charts and mind maps.  Data visualization tools are often used in conjunction with data mining tools.

  • GGOBI
    Open source visualization software.
  • GRAPHIZ
    Open source visualization software with several graph layout programs.
  • VTK
    Open source visualization program for 3D computer graphics and imaging.
  • CLACK GRAPHICAL ROUTER
    Designed expressly for undergrads. This software visualizes " network behavior and router internals"
  • IBM OPEN VISUALIZATION DATA EXPLORER
    "Open Visualization Data Explorer is a visualization framework that gives users the ability to apply advanced visualization and analysis techniques to their data"
  • XMDV
    Open source tool which allows visualization of multivariate data sets.
  • Many Eyes 
    Free web based data visualization.

Mapping Tools

Chemistry Tools

These are some tools that are designed to provide solution for problems unique to chemistry practitioners.

Statistical Packages

  • R
    R is a statistical package that provides a number of statistical and graphical features. Like the vast majority of Open Source Software it can be easily customized.
  • ESS
    "Emacs Speaks Statistics (ESS) is an add-on package for emacs-based text editors such as GNU Emacs and XEmacs. It is designed to support editing of scripts and interaction with various statistical analysis programs such S-Plus, R, SAS, Stata, and others".
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