Gaggle Components
Geese
Data Standards
Boss

Gaggle Blank Slate (2007-04)

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.
    • 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

Utility Geese

© 2007, Institute for Systems Biology, All Rights Reserved
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