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.

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. Restricted Data
   • Password required.
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. 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.
8. 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.
9. Analysis Tools
   • MeV MultiExperiment Viewer microarray data analysis tool.
     • For general information on MeV see the TM4 website.
   • 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 way of visualizing data plotted against coordinates on the genome. Tiling arrays and ChIP-chip data are a couple use cases.

Tutorials:

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