Category Cross-Omics>Pathway Analysis/Tools

Abstract Medusa is a Java application for visualizing and manipulating graphs of interaction, such as data from the STRING database (see G6G Abstract Number 20298).

It features an intuitive user interface developed with the help of biologists.

Medusa is optimized for accessing 'protein interaction' data from STRING, but can be used for any type of graph from any scientific field.

Medusa features/capabilities include:

1) Medusa displays up to ten (10) multiple edges concurrently between nodes using Bezier curves and allows users to add and delete nodes and edges by simply clicking the mouse.

2) Background images can be inserted to enhance figure quality.

3) Edges can be hidden or shown depending on the type of interaction.

4) Node properties can be described, such as color, annotation, position and shape.

5) Medusa requires No additional packages and runs on any machine with Java 1.4.2 or greater installed.

6) It runs as standalone and as an applet for use in web interfaces.

7) Graphs can be exported to image or postscript files.

8) Overall, Medusa is designed to be a simple and an intuitive tool for customization of interaction graphs of any kind.

With the ever-increasing mass of biological data, as exemplified by large-scale cross-species comparisons of proteins and genes, an easy visualization of the often highly complex linkage between, e.g. proteins becomes more and more important.

For instance, the interactions between core proteins and alternative functional modules of complexes (work in progress) can be represented as a graph of nodes (proteins) and edges (interactions between core and modules).

Other graphs of protein interaction may be more abstract; for instance, the STRING (‘search tool for the retrieval of interacting genes/proteins’) database predicts protein–protein associations and includes a variety of indirect (non-physical) evidence types.

The results from the STRING database can be studied using its web interface, or alternatively handled directly by the Medusa application, which is run on the client side.

The handling of large networks is made easier by layout algorithms and the option to hide or show certain edge types.

Moreover, nodes and edges can be deleted or added either manually via mouse clicks, or added directly from STRING.

Users can create their own data files which can then be easily appended to existing graphs. These data files are simply tab-delimited text fields describing edge relationships.

Used solely as a graph visualization tool, Medusa is designed to be immediately accessible, focusing on construction of figures.

Medusa is also available as an applet version for use directly in web pages.

This version has a lower degree of functionality, since the main goal is to allow an easy display of graphs from a web-based database.

It is already implemented in the STRING website and is planned to be incorporated into other web databases (work in progress).

The graph is simply passed to the applet as parameters, along with other preferences, making it highly suitable as an interactive enhancement of an existing web server.

Medusa has been used in a number of EMBL projects as an in-house tool, ranging from yeast cell cycle studies to genotype-phenotype links.

System Requirements

Any machine with Java 1.4.2 or greater installed.


Manufacturer Web Site Medusa

Price Medusa is distributed under the Gnu Public License and costs nothing. The only thing we (Sean Hooper, Peer Bork) ask is that you please cite us using: Hooper SD, Bork P. (2005) Medusa: a simple tool for interaction graph analysis. Bioinformatics. 2005 Sep 27

G6G Abstract Number 20299

G6G Manufacturer Number 100849