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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.
A JavaFx 8 educational application that will let you visualize digital and analog signals from a binary input and let you export the chart in SVG (Everything is in progress).
Digital: Bipolar, CMI, NRZ-L, NRZ-M, NRZ-S, Manchester, Manchester differential, Miller, MLT-3, pseudoternary, RZ, Unipolar.
Analog: Phase, Frequency, Amplitude.
...The algorithm for calculating GSH is called Pluton and the present
Java realization is based on two articles.
"Efficiently computing a linear extension of the sub-hierarchy of a
Concept Lattice" by Anne Berry, Marianne Huchard,
Ross M. McConnell, Alain Sigayret and Jeremy P. Spinrad.
"Performances of Galois Sub-hierarchy-building algorithms" by
Gabriela Arevalo, Anne Berry, Marianne Huchard,
Guillaume Perrot and Alain Sigayret
In you're in need of other GSH algorithms or their realizations in C++,
you might want to investigate a project called Galicia on sourceforge.
...