Gaggle Components
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Data Standards
Boss

The DOE/Archaea/MAGGIE Gaggle

The DOE/Archaea Gaggle

MAGGIE:   Molecular Assemblies, Genes, and Genomics Integrated Efficiently

For more information about the MAGGIE project see the MAGGIE website at the Scripps Institute.

For an integrated view of all MAGGIE organisms, check out the MAGGIE Data Viewer.

  1. Boss
  2. STRING-to-organism name translators (needed because STRING broadcasts non-standard names).
  3. View the cMonkey Maggie Tutorial C3 data
    • The tutorial demonstrates exploration of co-regulated gene clusters generated by the cMonkey biclustering algorithm using data from the MAGGIE project.
    • For more information see the cMonkey paper.
  4. Annotation
  5. Fractionation: Restricted Data
  6. Microarray Data
    • Adams Lab C1 data
    • Halo C3 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.
  7. Transcriptome structure: (Tiling array growth series.)

    Please note that these links download large data files (~60-190MB).

  8. Networks
  9. Orthology Translators

    Bug warning: the translator does not properly translate species.

  10. 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

Tutorials:

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