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

See All Activity >

Categories

Algorithms, Data Visualization

Follow EntOpt Layout

EntOpt Layout Web Site

Other Useful Business Software
Ship AI Apps Faster with Vertex AI Icon
Ship AI Apps Faster with Vertex AI

Go from idea to deployed AI app without managing infrastructure. Vertex AI offers one platform for the entire AI development lifecycle.

Ship AI apps and features faster with Vertex AI—your end-to-end AI platform. Access Gemini 3 and 200+ foundation models, fine-tune for your needs, and deploy with enterprise-grade MLOps. Build chatbots, agents, or custom models. New customers get $300 in free credit.
Try Vertex AI Free
Rate This Project
Login To Rate This Project

User Reviews

Be the first to post a review of EntOpt Layout!

Additional Project Details

User Interface

Java Swing, Plugins

Programming Language

Java

Related Categories

Java Algorithms, Java Data Visualization Software

Registered

2015-01-10
Report inappropriate content