SPINE Download Page

SPINE is a framework for Signaling-regulatory Pathway INference. The framework aims at explaining gene expression experiments in which a gene is knocked out and as a result multiple genes change their expression levels. This page contains the source code and the data files used in SPINE.

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This is the source code and data for all of the SPINE utilities. The source contains the c++ header and implementation files, as well as a script that convert the output to a "cplex" optimization problem. The data contains the network and the knockout data.

NOTE THAT BY DOWNLOADING THE SOURCE CODE AND DATA YOU ARE ACCEPTING THE FOLLOWING LICENSE AGREEMENT

License Agreement:	The computer software known as SPINE (or 'The Software') was created and developed in the course of research by Oved Ourfali, under the supervision of Dr. Roded Sharan, at the School of Computer Science, Tel Aviv University (`TAU`). TAU encourages the use of SPINE by researchers in academic institutions (`Licensee`) for non-commercial research purposes subject to the following terms and conditions: By downloading the software you and your institution agree to be bound by the terms below. 1. It is hereby agreed that all right title and interest in and to SPINE and any translations, adaptations, alterations, modifications or similar derivative of any of the foregoing and in and to any physical embodiment of SPINE and associated documentation vest exclusively in Tel-Aviv University and/or RAMOT - TAU Authority for Applied Research and Industrial Development Ltd. 2.1 Licensee is hereby granted a non-exclusive, non-transferable license to use SPINE for the sole purpose of performing non-commercial academic research. (Such research shall not include research sponsored by a commercial entity). 2.2. For the avoidance of doubt it is hereby clarified that the license to use SPINE as aforesaid does not include any obligation or undertaking to supply any accompanying services or improvements. 3. Licensee agrees not to distribute or transfer SPINE or any portion, copies or derivatives thereof, to another location or to any third party. 4. Licensee agrees not to make any copies except as necessary for his exercise of this license in his own laboratory. Any copy shall bear an appropriate copyright notice specifying the above-mentioned authors and proprietor. 5. Licensee agrees not to decompile, reverse engineer, disassemble, modify and/or create derivative works of SPINE. 6. Licensee acknowledges that SPINE is a research tool, still in the development stage. Hence, it is not presented as error free, accurate, complete, useful, suitable for any specific application or free from any infringement of any rights. The Software is licensed AS IS, entirely at the Licensee's own risk. 7. Nothing in this Agreement shall be deemed to be a warranty or representation by TAU, Ramot or the Researchers, in connection with SPINE and its use, including, without limiting the generality of the aforesaid, as to the accuracy, safety or fitness for any particular use. 8. The Researchers, TAU and/or Ramot shall not be liable for any damage, claim, demand, cost or expense of whatsoever kind or nature directly or indirectly arising out of or resulting from or encountered in connection with the use of SPINE by Licensee or any person receiving it from Licensee.
Source:	SPINE-src.zip
Data:	SPINE-data.zip

Reference: "SPINE: A Framework for Signaling-Regulatory Pathway Inference from Cause-Effect Experiments", by:
Oved Ourfali^a, Tomer Shlomi^a, Trey Ideker^c, Eytan Ruppin^a,b and Roded Sharan^a
^aSchool of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
^bSchool of Medicine, Tel-Aviv University, Tel-Aviv, Israel
^cDepartment of Bioengineering, University of California, San Diego, CA 92093, USA