Welcome to Visualization Lab

GML is a novel grid-layout algorithm that aims to clarify the network complexity according to its inherent modular structure. With the method of module-layout, GML optimizes the locations of modules to reduce visual complications effectively and is particularly suitable for visualizations of complex biological networks with modular feature.

Availability and Requirements

• Project name: Grid & Modular based Layout algorithm (GML)
• Project home page :https://hscz.github.io/Biological-Network-Visualization/
• Operating system (s) : Windows (32or64 bit version)
• Programming language : Java
• Other requirements : Java 1.6+
• License : Free for non-commercial use.

Download

GML:

The GML plugin and test networks can be downloaded from here.

GBL:

For comparison purpose, another grid-layout software GBL can be downloaded from here.

Hybrid grid layout:

The hybrid grid layout had been developed by Inoue et al., please refer to document: Inoue K, Shimozono S, Yoshida H, Kurata H: Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps. PLoS ONE 2012, 7(6):e37739..

The tool of hybrid grid layout can be downloaded from here.

Note

All tools and example networks can be found at the website, and these can constitute the minimal data necessary to replicate the results in our manuscript.(2019-02-04 latest update)