KeiRo

KeiRo is a package for generating biological pathway diagrams, which contain the following features:

• Harmony is a harmonized layout algorithm for biological pathways.
• Lens is a lens technique for exploring diagrams semantically.
• Metabopolis is a new layout algorithm for biological pathways, which has been developed by Hsiang-Yun Wu, Martin Nöllenburg, and Ivan Viola, in the group Research Unit of Computer Graphics at TU Wien in Vienna, Austria. The c++ library was developed by Hsiang-Yun Wu.

How to cite?

• Hsiang-Yun Wu, Martin Nöllenburg, Filipa L. Sousa, and Ivan Viola, Metabopolis: Scalable Network Layout for Biological Pathway Diagrams in Urban Map Style, BMC Bioinformatics, Vol. 20, No. 1, p. 187, 2019. [Paper] [Video]

Installing

Prerequisites

• cmake 3.10+
• qt 5.13
• Boost Graph Library 1.71
• libsbml 5.17
• libSBGN 2.0
• Eigen3 3.3
• CGAL 4 4.14.3

Build

Clone the KeiRo repository into a directory KeiRo.

$ git clone KeiRo
$ cd KeiRo
$ mkdir build
$ cd build
$ cmake ../
$ make

Using KeiRo

$ ./KeiRo

Tested environment

• Ubuntu 20.04LTS, 22.04 LTS
• Mac OS 10.12

Acknowledgement

The project leading to this submission has received funding from the European Union Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 747985 and from the Vienna Science and Technology Fund (WWTF) through project VRG11-010.