Medical Systems Biology

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JANet

JANet (Jmol AgeFactDB Network-viewer) is a specialized Jmol-based 3D network viewer for the visualization of ageing-related network data from AgeFactDB.

 JANet 3D viewer interface screenshot

Features

  • Interactive 3D network visualization (rotate, zoom, etc.)
    • 2D representation
    • Stereo representation (e.g.: side by side, red/cyan)
    • 3D beamer mode (condensed side by side stereo, converted for shutter glasses)
      JANet 3D beamer mode example
  • Ageing-related network data (AgeFactDB)
    • Lifespan observations
    • Ageing factors
    • Augmentation nodes (e.g.: allele types, citations)
  • Augmentation with external domain knowledge
    • Gene Ontology (GO)
    • KEGG Pathways
  • Genes of interest analysis (e.g.: differentially expressed genes)
  • Scripting language
    • Jmol scripting language
    • JANet-specific API

Installation

The viewer can be started directly from the server at http://sysbio.uni-ulm.de/software/janet
or downloaded including all necessary network data for local installation
(http://sysbio.uni-ulm.de/software/janet/janet.zip).

For a local installation there are two options:

  1. Extract the archive somewhere in the file system.
  2. Install a web server locally and extract the archive somewhere below the server root directory.

Option 1:  JANet can be started by opening the file \textit{index.html} from the top level directory in a web browser as a local file. In some browsers, like Safari, this requires to switch off a default restriction for local file usage. The Javascript version of JANet will not work in browsers that prevent loading local binary files using Javascript, like Safari and Opera.

Option 2: JANet can be started by adding the relative directory path of the top-level viewer directory to the server name \textit{localhost} for the local web server and open the web address in a web browser.
  (Example:  http://localhost/tools/janet)

Citing JANet

To cite the network viewer in publications, use:


[submitted, no publication available yet]

Latest News

Our paper "A Boolean Network of the Crosstalk Between IGF and Wnt Signaling in Aging Satellite Cells" has been published in Plos One.

Our paper "Long-lived rodents reveal signatures of positive selection in genes associated with lifespan" has been published in Plos Genetics.