Software

The Benfey Lab runs a publicly accessible Maven repository. For each published Java application or library, this repository contains the license agreement, executable jar file, javadoc, and source code. A human-accessible interface for this repository is located at Benfey Lab Maven Repository. The primary goal of this repository, however, is to provide programmatic access to published Java software.

A human-oriented website is located at Benfey Lab Software. It provides documentation for published software and links to the Maven repository where files can be downloaded.



ChipEnrich

This software can be used to identify the biological significance of genes associated with dominant expression patterns. This software is used to identify statistically significant enriched Gene Ontology (GO) categories, transcription factor families, and biological processes that have been identified via microarray analysis.

This software was used in Brady et al., 2007. A detailed description of ChipEnrich software, including the method used and input files structure, is given in Orlando et al., 2008.

ChipEnrich is distributed as an executable jar file. To run it, you need Java Runtime Environment (JRE) version 1.5 or later. When you have JRE installed and chipenrich-1.0.jar downloaded:

  1. From command prompt, execute javaw -jar path/chipenrich-1.0.jar (or just doubleclick chipenrich-1.0.jar if your shell associates jar files with JRE).
  2. Select "Start..." from "File" menu.
  3. Select query list (see Orlando et al., 2008 for details regarding input format).
  4. Results will be output in the same directory that you selected your query files in.

Download ChipEnrich (executable jar file)



Dominant Pattern Identification (DPI)

This software was used in Brady et al., 2007. A detailed description of Dominant Pattern Identification software, including the method used and input files structure, is given in Orlando et al., 2008.

DPI software is distributed as Perl script. The Perl script communicates to the user to obtain required parameters (input and output file names, modes, etc.) and generates an R program. The generated R program can be later executed on the user's computer or submitted for execution to a cluster of computers.

The Perl script provides extensive help and does not perform any non-reversable action without explicit confirmation from the user. -- So, it is safe to run the Perl script to learn more about this software.

To run DPI software, one needs:

  • Perl interpreter (on Unix machine, it is installed by default).
  • R interpreter (is required only for the second step -- execution of generated R program).

To install DPI software on your computer:

  • Download zipped Perl script using link below.
  • Unzip downloaded file -- this will produce file PatternFinding-MasterScript.pl. On Unix machines, the recommended directory to place this file into is ~/bin/. On Windows machines, the recommended directory to place this file into is C:\Programs\DominantPatternIdentification\.
  • On Unix machine, set execute permission for the script file (chmod 750 ~/bin/PatternFinding-MasterScript.pl).

To run DPI software on your computer:

  • On Unix machines:
    • Change current directory to the one containing your input files.
    • Type PatternFinding-MasterScript.pl in terminal window.
  • On Windows machines:
    • Open "Command Prompt" window.
    • Change current directory to the one containing your input files.
    • Type perl C:\Programs\DominantPatternIdentification\PatternFinding-MasterScript.pl

You can rename the Perl script to use shorter name if you prefer.

Download Dominant Pattern Identification program (zipped Perl script)