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README.md

cyTRON/JS

cyTRON in an application for cancer progression analysis. It is an interface to the R library TRONCO and it supports both the visualization of already constructed models and the creation of new analysis.

Getting started

This application has been developed using NodeJS. In order to run it it is necessary to install the following:

  • Node.js
  • R
  • Java: make sure that the enviroment variables are set properly (MAC, Windows)

Installing

  • Clone this repository in a folder in your local machine
  • Open the command prompt and cd into the folder
  • Run the command npm install
  • Type the following: npm start
  • For the time being, open the browser and navigate to http://localhost:3000/.

Note: no additional R package is necessary, any missing package will be automatically installed on the application's first run.

Google Summer of Code

cyTRON/JS was developed within the GSoC 2018 program, in collaboration with the NRNB organization.

During the program the following functionalities have been implemented:

  • Graph visualization and manipulation: this was accomplished using Cytoscape.js and its extensions.
  • Javascript-R communication: this was accomplished using the npm package js-call-r. In particular it is possible to:
    • select input data in the formats suported by TRONCO (MAF, GISTIC and a custom boolean table)
    • Select an input file with driver mutations
    • Select a file with information about clusters into which the data needs to be splitted
    • Reconstruct the model using TRONCO's algorithms
    • Visualize the contructed model.

Project structure

The web application was built using the Framework Express. The code is divided as follows:

  • Controller: this is the folder where the functions to hadle the different HTTP requests are implemented. In particular it contains the R and JavaScript code necessary for the communication between cyTRON/JS and TRONCO.
  • View: this is the folder which contains the interface.
  • Routes: in this folder there is the code which maps each HTTP request to the corresponding function in the controller.
  • Public: this is the folder which contains CSS and client-side JavaScript, which handles graph visualization.