BIMIB has entered as a “mentor group” in the latest Google Summer of Code under the auspices of the National Resource for Network Biology.

BIMIB is welcoming applications to work on cyTRON: a Cytoscape app. The link to the NRNB project page is below:

https://github.com/nrnb/GoogleSummerOfCode/issues/52

Background

The BIMIB group has constructed a series of algorithms that reconstruct cancer progression models starting from cross-sectional data. See TRONCO BioConductor for more information. The progression models are reconstructed using a theory of “probabilistic causation” rooted in Suppes’ work. At the time of this writing, the R TRONCO library produces a DAG data-structure encoded in an adjacency matrix that is statically visualized using the R graphviz interface. A TRONCO to Cytoscape bridge is already available, based on RServe.

Goals

In order to improve the visualization of the progression models, we have started to develop cyTRON, a Cytoscape app to visualize them. We would like to propose cyTRON further development as a GSoC project for a motivated programmer. The main goal will be to read in the progression model DAG data-structure with all its annotations over the RServe bridge (or, possibly, over a new cyREST bridge) and to display it in the main Cytoscape window. The Cytoscape DAG display will also allow for the linking of web-based resources (e.g., gene annotations), in order to provide more information for the user.

Difficulty level: 2

Prior experience with Cytoscape app development or extensive Java and graph theory experience highly recommended.

Technologies Involved

Cytoscape, RServe, R.

Potential Mentors

Marco Antoniotti (mailto:marco.antoniotti [you-know-the-drill!] unimib.it)