These webstarts will invoke the Gaggle with no data loaded. Load your own data and analyze it using the Gaggle.

1. Start Gaggle Boss
   • Optionally start the Gaggle Boss first.
2. Start DMV - The Data Matrix viewer gives a spreadsheet-like view of tabular data.
   • Load your microarray data:
     1. File > Load > Tab-Delimited file (Browse to the appropriate directory and load a file of this format.)
     2. For more information on using DMV go here.
3. Start Cytoscape 2.6 or Cytoscape 1.x
   1. Load your network:
      • (2.6): File|Import|Network
      • (1.x): File|Load|Interaction
   2. Browse to the appropriate directory and load a network file in this format.
   3. For more information on using Cytoscape go here.
4. Start Annotation Goose
   • Load your annotations:
     1. File > Load Annotation File > Browse to a tab-delimited file of this format.
5. Start Translator Goose
   • Load custom mappings in tab-delimited text format described here.
6. Analysis Tools
   • MeV MultiExperiment Viewer microarray data analysis tool.
     • Recommended: install MeV from the TM4 website.
     • Older version: MeV 3.1
   • R statistics package
     • If R and the Gaggle package are not installed, see these instructions.
     • Connect R to the Gaggle, as described in 'Startup'.
       • At the R prompt, type these commands (in R 2.4.x):

         
         library(gaggle)
         source("http://gaggle.systemsbiology.net/R/gaggleUtil.R")
         gaggleInit()
         

     • See the cribsheet for quick instructions on how to accomplish common tasks using R and the R goose.
   • Firegoose
     • If the Firegoose extension is not installed, see these instructions.
     • Start the Firefox browser.
     • Use the Paster Application to paste data into Firegoose.
   • Genome Browser
     • The genome browser is a tool for visualizing data plotted against coordinates on the genome. Tiling arrays and ChIP-chip data are a couple use cases.
   • BioTapestry
     • BioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks. More information on using BioTapestry with Gaggle.

Utility Geese

• Sample Goose
• Boss2 - for testing only