FASPAD: A Tool for the Detection of Linear Signaling Pathways in Protein Interaction Networks

Introduction

From this page you can download a tool to detect signaling pathway candidates in protein interaction networks as described in

• Falk Hüffner, Sebastian Wernicke, and Thomas Zichner
  FASPAD: Fast Signaling Pathway Detection.      
  Bioinformatics Applications Note, 23(13): 1708–1709, 2007.

It can be also used to find minimum-weight simple paths of a user-specified length in arbitrary networks.

The tool is based on an implementation of the algorithms described in the paper

• Falk Hüffner, Sebastian Wernicke, and Thomas Zichner
  Algorithm engineering for color-coding to facilitate signaling pathway detection.      
  Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC 2007). Advances in Bioinformatics and Computational Biology 5, 277–286, Imperial College Press, January 2007.

License

The program is distributed under the terms of the GNU Public License (GPL), version 2 or (at your option) any later version. See the file COPYING or http://www.gnu.org/copyleft/gpl.html for details. FASPAD uses the GraphViz library version 2.8 by AT&T Research Labs, which is distributed under the Common Public License (CPL). Therefore, as a special exception, you are allowed to link FASPAD with graphviz (or modified versions of graphviz that use the same license) and to distribute the resulting executable (providing you comply with the other terms of the GPL and CPL).

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.

Downloads

Last updated on April 15, 2007.

		Download zipped executable for Linux (GTK/i386) here (8.1MB).
		Download zipped executable for 32-bit Windows (i386) here (2.5MB). Unfortunately, the PostScript format (for saving of result graphs) is not yet supported in the Windows version, but *.png as well as *.dot work fine.
		Download the documentation here (380KB).
		Download the source code here (70KB).

As test data you can use the protein interaction networks from yeast and drosophila which both were obtained from http://bioinf.ucsd.edu/~sbandyop/GR/.

Authors

The program was written by Falk Hüffner (homepage, email) and Thomas Zichner (email) in collaboration with Sebastian Wernicke (homepage, email).

This work was supported by the Deutsche Telekom Stiftung and the Deutsche Forschungsgemeinschaft (DFG), projects PEAL (Parameterized Complexity and Exact Algorithms, NI 369/1), OPAL (Optimal Solutions for Hard Problems in Computational Biology, NI 369/2), and PIAF (Fixed-Parameter Algorithms, NI 369/4).

            

Epilogue

Happy pathway detecting!

Thomas Zichner (email)
Jena, February 23rd, 2007.