urszulaczerwinska / dedal

DeDaL (Data-Driven network Layout) is a Cytoscape 3.0 [1] app developed by the Computational Systems Biology of Cancer group in Bioinformatics Laboratory of Institut Curie (Paris).

DeDaL

DeDaL (Data-Driven network Layout) is a Cytoscape 3.0 app developed by the Computational Systems Biology of Cancer group in Bioinformatics Laboratory of Institut Curie (Paris).

The knowledge on molecular interactions in living cells is usually represented in the form of network diagrams, depicting, for instance, protein-protein interactions, biochemical reactions or more abstract influences of some molecule onto another molecules, etc. Providing an insightful layout for such diagrams is not a trivial problem. On the other hand, large amount of data is produced by application of high throughput biotechnologies. There is an urgent need of developing new methods for integrating the information provided in biological diagrams with the multidimensional -omics datasets. Classically, high-throughput data are mapped on top of the network layouts computed based on the network structure.

DeDaL can be used entirely in Cytoscape or in a command line mode or in a combination of both.

Step by step tutorial is available at http://bioinfo-out.curie.fr/projects/dedal/.

For complete description please refer to http://www.biomedcentral.com/1752-0509/9/46.

A non-biological application to International Currency Exchange data can be found at http://urszulaczerwinska.github.io/works/DeDaL.

##Installation To install in the Cytoscape 3.0

1. Open Cytoscape 3.0
2. Application manager -> Install from file...
3. Load DeDaL.jar

If you want to compile yourself:
git clone https://github.com/sysbio-curie/DeDaL/ .
ant jar
DeDaL.jar will appear in ./build/

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