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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.

Finally, the binary release of the version 0.2.5 is out. Now, Atheris comes with an extensible, modular plug-in architecture, i.e. you can easily write your own graphical analyzer for Atheris. The documentation on how to write you own analyzer will follow in the next days. If you are running a non Debian-based Linux, download the zip file and follow the instructions in the README file. If you have problems, want to contribute your code or have some special needs, let us know and send...