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

EntOpt plugin

Project Activity

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Categories

Algorithms, Data Visualization

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Additional Project Details

User Interface

Java Swing, Plugins

Programming Language

Java

Related Categories

Java Algorithms, Java Data Visualization Software

Registered

2015-01-10
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