BMTK: a toolkit for determining modules in biological bipartite networks

Abstract

Background: Module detection is widely used to analyze and visualize biological networks. A number of methods and tools have been developed to achieve it. Meanwhile, bipartite module detection is also very useful for mining and analyzing bipartite biological networks and a few methods have been developed for it. However, there is few user-friendly toolkit for this task.

Methods: To this end, we develop an online web toolkit BMTK, which implements seven existing methods.

Results: BMTK provides a uniform operation platform and visualization function, standardizes input and output format, and improves algorithmic structure to enhance computing speed. We also apply this toolkit onto a drug-target bipartite network to demonstrate its effectiveness.

Conclusions: BMTK will be a powerful tool for detecting bipartite modules in diverse bipartite biological networks.

Availability: The web application is freely accessible at the website of Zhang lab.

Author summary

Networks are becoming important tools for representing biological systems. BMTK is designed to detect bipartite modules for resolving bipartite biological networks. BMTK provides a uniform operation platform and visualization function.

Graphical abstract

Keywords

network biology / module detection / biological bipartite networks

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SUPPLEMENTARY MATERIALS

The supplementary materials can be found online with this article at 10.1007/s40484-018-0132-y.

ACKNOWLEDGEMENTS

This work has been supported by the National Natural Science Foundation of China (Nos. 61621003, 61422309, 61379092 and 11661141019), the Strategic Priority Research Program of the Chinese Academy of Sciences (CAS) (XDB13040600) and CAS Frontier Science Research Key Project for Top Young Scientist (QYZDB-SSW-SYS008).

COMPLIANCE WITH ETHICS GUIDELINES

The authors Bei Wang, Jinyu Chen and Shihua Zhang declare that they have no conflict of interests.

This article does not contain any studies with human or animal subjects performed by any of the authors.

RIGHTS & PERMISSIONS

2018 Higher Education Press and Springer-Verlag GmbH Germany, part of Springer Nature