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• Download and Installation
  ...installed on your machine, you can just type "ant run" in the geWorkbench root directory and the program will be built and run. Ant can be downloaded fro
  25 KB (3,898 words) - 15:50, 22 December 2016
• FAQ
  ...utions using Ant, you can edit the build.xml file found in the geWorkbench root directory to alter the memory requested using the jvmarg value="-Xmx1024M" ...stallAnywhere-generated install file contain a configuration file in their root directory called UILauncher.lax. Make the changes like the following to t
  8 KB (1,336 words) - 18:39, 23 January 2015
• Style Guide
  This section describes the directory structure of the project. The root directory structure contains eclipse project file, the <tt>java.policy</tt>
  7 KB (1,162 words) - 13:58, 1 March 2012
• A Simple Plugin
  ...rs. Each class specified must be assignable to <code>DSDataSet</code>, the root class of all data sets. Leaving the annotation out completely will result i
  11 KB (1,494 words) - 11:08, 16 July 2013
• Promoter Analysis
  ** Sqrt(n) - if checked, set the pseudocount to be the square root of (n). This option is not recommended, see discussion below. ...good value "for practical uses". They do not recommend use of the square root of the total count.
  18 KB (2,714 words) - 19:19, 22 January 2014
• ARACNe
  ...scovery mode, it will look for the dataset-specific parameter files in its root directory. If the files are not found (Preprocessing has not been run), de ...ed Bandwidth (FBW) algorithm''' - two files are written to the geWorkbench root directory, one containing parameters for calculating the kernel width, and
  29 KB (4,490 words) - 17:26, 30 January 2015
• Comments on geWorkbench
  :save a workspace as non-root in e.g. /etc => no error message is shown => no file is created => no excep
  78 KB (12,333 words) - 13:35, 11 September 2008
• MINDy
  ...RACNe. Files with those names, if present in the geWorkbench installation root folder, will override any other dataset-specific configuration files for AR
  26 KB (4,164 words) - 18:52, 22 January 2014
• Tutorial - temp
  ...scovery mode, it will look for the dataset-specific parameter files in its root directory. If the files are not found (Preprocessing has not been run), de * Fixed Bandwidth (FBW) algorithm - two files are written to the geWorkbench root directory, one containing parameters for calculating the kernel width, and
  15 KB (2,337 words) - 15:00, 15 July 2009
• Hierarchical Clustering
  ...nts, at each step building up a branched structure that converges toward a root that contains all points. The resulting graph tends to group similar items * '''Euclidean''' - The direct, point-to-point distance is calculated (square root of the sum of square differences).
  9 KB (1,341 words) - 16:39, 19 March 2015
• Gene Ontology Term Analysis
  ...have more than one parent, and hence there can be multiple paths from the root by which a term can be reached. The Ontologizer code uses the "true path"
  11 KB (1,663 words) - 14:14, 23 April 2014
• Previous Release Issues
  ...However, only users with administrator privileges can install to the c:\ root directory. Instead, users with regular user permissions should install to
  22 KB (3,413 words) - 18:25, 22 January 2015
• Release Descriptions
  root directory (currently for Windows and Mac OS X only). These files allow ...lity to specify pseudocount or select previous hard-coded option of square root of number of sequences.
  34 KB (5,033 words) - 11:27, 22 December 2016
• PreviousReleases
  ...lity to specify pseudocount or select previous hard-coded option of square root of number of sequences.
  27 KB (3,966 words) - 17:27, 15 July 2013
• GeWorkbench-web/Hierarchical Clustering
  ...nts, at each step building up a branched structure that converges toward a root that contains all points. The resulting graph tends to group similar items * '''Euclidean''' - The direct, point-to-point distance is calculated (square root of the sum of square differences).
  7 KB (1,028 words) - 12:56, 27 April 2015