PubArray

Current Version 1.0.0 (April 5th, 2010)

About PubArray

PubArray is a desktop application that allows you to turn the analyzed results of your microarray experiment into a web application which is accessible via your browser. Detailed information about PubArray functions can be found on the Help page, below is a summary of PubArray features:

  • Imports microarray intensity values and test statistics as exported by J/maanova
  • Imports per-probeset graphs: this feature is useful for example if you have generated eQTL plots per-probeset or if you have custom probeset intensitly plots that you want to include in your web application
  • Allows for the import of any number of probeset annotation files
  • Allows users to search, sort, subset and download experiment data
  • Generates probeset intensity graphs which allow the user to sort or group arrays based on experiment design factors

PubArray generates a WAR (Java Web Application) file as its output. You can deploy PubArray using the Apache Tomcat server.


Warranty Disclaimer and Copyright Notice

The Jackson Laboratory makes no representation about the suitability or accuracy of this software for any purpose, and makes no warranties, either express or implied, including merchantability and fitness for a particular purpose or that the use of this software will not infringe any third party patents, copyrights, trademarks, or other rights. The software are provided "as is".

This software is provided to enhance knowledge and encourage progress in the scientific community. This is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

The source code for PubArray can be found at the source code repository on github

Installation

Requirements:

  • Java 5.0 or greater (all Mac OS X computers come preinstalled with Java)
  • RAM: memory requirements will vary depending on the size of the data that you are analyzing and the type of analysis you perform, but 2Gb or greater is recommended
  • Supported operating systems:
    • Mac OS X 10.5.8 or greater
    • Windows XP (Windows Vista and Windows 7 should also work but are untested)

After you have ensured that your computer meets these requirements you can use the following link to launch the PubArray installer




Help and Contact Information

For help on using PubArray visit the online help documentation

For any problems, questions, or suggestions please send email to keith.sheppard@jax.org.