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).
   • STRING to Pyrococcus
   • STRING to Halo
   • STRING to Sulfolobus
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
   • Pyrococcus furiosus (from TIGR)
   • Sulfolobus solfataricus (from TIGR)
   • Halobacterium sp. (from TIGR)
   • NCBI annotations for each organism.
   • Blank Annotation Goose
     • Load your own annotations by the menu option File|Load Annotation File
     • Accepts tab-delimited files in a format described here.
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).

   • Halobacterium salinarum NRC-1
   • Methanococcus maripaludis (legend) (Maggie member labs only.)
   • Pyrococcus furiosus (Maggie member labs only)
   • Sulfolobus solfataricus (Maggie member labs only.)
   • S. solfataricus proteomics
   • Desulfovibrio vulgaris Hildenborough
8. Networks
   • Halobacterium NRC-1
   • Prolinks networks (see the Prolinks paper and website for more information):
     • Halobacterium Prolinks
     • Sulfolobus Prolinks
     • Pyrococcus Prolinks
   • Start Cytoscape 2.x (NOT YET AVAILABLE) or Cytoscape 1.x
     1. Load your network:
        • (2.3): 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 see on using Cytoscape go here.
9. Orthology Translators

   Bug warning: the translator does not properly translate species.

   • (based on COG, Clusters of Orthologous Groups of proteins)
     • Sulfolobus - Halobacterium
     • Halobacterium - Pyrococcus
     • Pyrococcus - Halobacterium
     • Pyrococcus - Sulfolobus
   • (based on Component 6 data)
     • Halobacterium to Sulf. or Pyro.
     • Pyrococcus to Halo. or Sulf.
     • Sulfolobus to Halo. or Pyro.
10. 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.

Tutorials:

• Using Gaggle to integrate data from multiple MAGGIE Components
• cMonkey and MAGGIE Gaggle Demo/Tutorial