Gaggle - H. pylori

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The Gaggle paper in BMC Bioinformatics

H. pylori Gaggle

Boss
DMV (data matrix viewer) w/ public H.py microarray data from Stanford.
Small flagellar-related network (23 genes) 'Prolinks'
Cytoscape Networks
Cluster viewer (provides additional information on biclusters)
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.

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