Browse Code
The goal of this project is to implement a graph layout / network visualization algorithm as a Java plugin for Cytoscape (http://cytoscape.org/), using a recently published relative entropy optimization based method, called Unified Data Representation (Kovács IA et al. Sci Rep. 2015). If you are using the plugin, please cite:
Ágg B, Császár A, Szalay-Bekő M, Veres DV, Mizsei R, Ferdinandy P, Csermely P and Kovács IA (2019) The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks, Bioinformatics 35(21):4490-4492
https://academic.oup.com/bioinformatics/article/35/21/4490/5475596
Our detailed Tutorial on the use of the plugin: https://suopte.com/entopt_2_1_tutorial_20200518.pdf
A video about the version 2.1: http://suopte.com/entopt_2_1_tutorial_video.mp4
Don't hesitate to send any questions, comments or bug reports also to agg.bence {at} med.semmelweis-univ.hu.
Features
- Relative Entropy Optimization
- Network layout
- Written in Java
- Cytoscape plugin
Project Samples
