# cyTRON and cyTRON/JS: two Cytoscape-based applications for the inference of cancer evolution models

## TL;DR

This paper introduces two Cytoscape-based tools, cyTRON and cyTRON/JS, for visualizing and manipulating cancer evolution models derived from genomic data, enhancing cancer research capabilities.

## Contribution

The paper presents two novel applications, one in Java and one in JavaScript/R, for cancer evolution model inference and visualization, integrating with public databases.

## Key findings

- Two new Cytoscape applications for cancer evolution modeling
- Tools are publicly available and easy to integrate with genomic data
- Enhanced visualization and interaction with cancer progression models

## Abstract

The increasing availability of sequencing data of cancer samples is fueling the development of algorithmic strategies to investigate tumor heterogeneity and infer reliable models of cancer evolution. We here build up on previous works on cancer progression inference from genomic alteration data, to deliver two distinct Cytoscape-based applications, which allow to produce, visualize and manipulate cancer evolution models, also by interacting with public genomic and proteomics databases. In particular, we here introduce cyTRON, a stand-alone Cytoscape app, and cyTRON/JS, a web application which employs the functionalities of Cytoscape/JS. cyTRON was developed in Java; the code is available at https://github.com/BIMIB-DISCo/cyTRON and on the Cytoscape App Store http://apps.cytoscape.org/apps/cytron. cyTRON/JS was developed in JavaScript and R; the source code of the tool is available at https://github.com/BIMIB-DISCo/cyTRON-js and the tool is accessible from https://bimib.disco.unimib.it/cytronjs/welcome.