Gaggle

1. Optionally start a Gaggle Boss
2. Annotations
   • TIGR Annotations
3. Cytoscape Networks
   • network (edges from Rich Bonneau).
4. Microarray Data
   • Blank DMV. Use the Data Matrix Viewer to load your own 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.
5. 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.

External Links

• NCBI Taxonomy:
  • Haloarcula (2237)
  • Haloarcula marismortui (2238)
  • Haloarcula marismortui ATCC 43049 (272569)
• TIGR Comprehensive Microbial Resource