FANMOD: a tool for fast network motif detection


FANMOD screenshot

Introduction

From this page you can download a tool to detect network motifs as described in

  • S. Wernicke and F. Rasche.
    FANMOD: a tool for fast network motif detection.   PDF  (c) Oxford University Press 
    Bioinformatics, 22(9):1152–1153, 2006.

The tool was written by Sebastian Wernicke (homepage, email) and Florian Rasche. It is based on an implementation of the algorithms described in the paper

  • S. Wernicke.
    Efficient detection of network motifs.   PDF   (c) IEEE 
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(4):347–359, 2006.

and is much faster than any other available motif detection tool, especially for larger motifs of size >4. Additionally, it allows for the detection of network motifs in colored networks.

License

You may use FANMOD for all of your research purposes as long as you do the following:

  • You acknowledge its use in any published work that fully or in part derives its results from its usage. (If you wish to make a bibliographical reference to the tool, please consider citing the Bioinformatics article for that purpose. For references to the algorithm, please cite the WABI paper.)
  • You do not sell anything that is based on or derived from it.

Absolutely no guarantees or warranties are made concerning the suitability, correctness, or any other aspect of the distributed files. Any use is at your own risk. This software uses the nauty program version 2.2 by Brendan McKay; note that hence nauty's license restrictions also apply to your use of FANMOD.

Downloads

Last updated on December 23rd, 2006.

  Linux logo

Download zipped executable for Linux (GTK/i386) here.

  Mac OS logo

Download zipped executable for Mac Os X here. Big thanks go to Davide Cittaro (Istituto FIRC di Oncologia Molecolare in Milan, Italy) for his work on this version.

  Windows logo

Download zipped executable for 32-bit Windows (i386) here.

  Documentation logo

Download the documentation here.

Some testdata is available from the webpage of Uri Alon at the Weizmann Institute here.

Tomer Benyamini (email), Yoav Teboulle, and Eyal Zernichov of the School for Computer Science at Tel Aviv University have created a command-line version of FANMOD, the source of which can be obtained here (RAR-compressed Archive).

Source

We had some people experience problems with the Linux version of FANMOD because different distributions contain different libraries. Therefore we make the source available, but under some restrictions:

  • By downloading the source of FANMOD, you agree to use it for the sole purpose of compiling it on your machine.
  • You must not make any modifications to the code or use it for software development of any kind without our prior explicit consent in writing.
  • You may not publish the source or any derivaties from it in any way. The source must not be used to build a motif detection tool intended for publishing.
  • FANMOD should be recognized in any published work that is derived from using the source.

If this seems agreeable to you, you can download the FANMOD source here. The ZIP-file also contains a compile script for the GNU gcc/g++ compiler, assuming you have a working version of the wxWidgets framework version 2.6 installed. Please understand that we cannot give any support concerning the compilation - it works fine on our machines. :)

If you want to download the C++-sourcecodes mentioned in the WABI paper, these are available

  • here (implementation of RAND-ESU) and
  • here (implementation of DIRECT algorithm for subgraph concentrations).

Both sources have been written for and tested with the GNU gcc/g++ compiler collection. Thanks to Sergi Valverde (homepage, email) at the Universitat Pompeu Fabra, Barcelona, Spain, there is also a version of the RAND-ESU code available for compilation with Microsoft Visual C++, it can be downloaded here.

Note that the subgraph concentration tool is only a proof-of-concept and much less mature and tested than the motif detection tool. Since the release of FANMOD, both sources are no longer actively maintained.

Authors

The program was written by Florian Rasche and Sebastian Wernicke (homepage, email). Sebastian Wernicke's research is funded by a scholarship from the Deutsche Telekom Stiftung. Florian Rasche's position as a student research assistant is funded by the Deutsche Forschungsgemeinschaft, project PEAL (Parameterized Complexity and Exact Algorithms), NI 369/1.

 Deutsche Telekom Stiftung          German National Academic Foundation 

Epilogue

Happy motif detecting!

Sebastian Wernicke (homepage, email)
Jena, July 9th, 2006.