bmotif: counting motifs in bipartite networks

Overview

bmotif is software to count occurrences of motifs in bipartite networks, as well as the number of times each node appears in each unique position within motifs. bmotif considers all 44 unique bipartite motifs up to six nodes and all 148 unique positions within these motifs. It is available in R, MATLAB and Python. bmotif was originally developed to analyse bipartite species interaction networks in ecology but its methods are general and can be applied to any bipartite graph. The code is released under the MIT license.

Motif and motif position dictionary

The motifs corresponding to each motif ID and the positions corresponding to each motif position ID can be found in Simmons, B. I., Sweering, M. J. M., Schillinger, M., Dicks, L. V., Sutherland W. J., Di Clemente, R. bmotif: a package for motif analyses of bipartite networks. Methods in Ecology and Evolution (accepted). These were defined following Baker et al (2015) Appendix 1 Figure A27.

Dependencies

bmotif is written in Python 2.7 and uses the following modules:

• numpy
• pandas

Scripts

• BMotifs.py: contains functions for counting the occurrences of motifs and the number of times each node appears in each unique position within motifs
• guide.ipynb: Shows how to use the two main functions on a simple example network

License

The code is released under the MIT license (see LICENSE file).

Citation

If you use the package in your work, please cite: Simmons, B. I., Sweering, M. J. M., Schillinger, M., Dicks, L. V., Sutherland W. J., Di Clemente, R. bmotif: a package for motif analyses of bipartite networks. Methods in Ecology and Evolution (accepted)

References

Baker, N.J., Kaartinen, R., Roslin, T. and Stouffer, D.B., 2015. Species’ roles in food webs show fidelity across a highly variable oak forest. Ecography, 38(2), pp.130-139.