Discovering Pathways by Orienting Edges in Protein Interaction Networks

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Java source code (version 1.1.0) implementing all Maximum Edge Orientation (MEO) algorithms described in the paper can be downloaded here. The latest source code is also available on GitHub. By downloading this software, you agree to the terms of the license below (New BSD License). If you use this software in a publication, please cite:
Discovering Pathways by Orienting Edges in Protein Interaction Networks
Anthony Gitter, Judith Klein-Seetharaman, Anupam Gupta, Ziv Bar-Joseph.
Nucleic Acids Research. 39:4, 2011.

Contact Anthony Gitter with any questions or comments about the code or to report a bug.

All versions (version log):
Version 1.1.0
Version 1.0.0

The MIN-k-SAT-based orientation algorithm relies on the lp_solve Mixed Integer Linear Programming solver, which is not distributed with our Java code and can be downloaded here. Instructions for installing lp_solve and using it with the Java code via the JNI API can be found here. lp_solve is no longer required by default.

The MAX-k-CSP-based algorithm uses toulbar2, which is described here and available for download here. There is no JNI wrapper for toulbar2, thus our orientation algorithm will generate a weighted CSP instance in the XML XCSP format, use toulbar2 to solve the CSP, and read the CSP solution to the orient the network.

Copyright (c) 2009, Anthony Gitter All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of Carnegie Mellon University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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