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Pash Download Page

Pash is an implementation of the Positional Hashing Method for sequence comparison, as described in:

     Coarfa, C. and Milosavljevic,A (2008). Pash 2.0: Scaleable Sequence Anchoring for Next-Generation Sequencing Technologies. Pacific Symposium on Biocomputing 13:102-113
     Kalafus KJ, Jackson AR, and Milosavljevic A (2004). Pash: Efficient Genome-Scale Sequence Anchoring by Positional Hashing. Genome Research 14: 672-678

To obtain the Pash program source code and accompanying tools, please read the License Agreement below and then follow the instructions at the end of this page.

COMMERCIAL LICENSING INFORMATION

Please contact the Baylor College of Medicine Office of Technology Administration, at 713-798-6821 or ota@bcm.tmc.edu, or Stewart Davis, at sdavis@bcm.tmc.edu, for information about obtaining a license to use this software in non-academic/for-profit institution.

ACADEMIC LICENSE AGREEMENT

This Academic License Agreement (Agreement) has been adopted for use by Baylor College of Medicine (BAYLOR), a Texas non-profit corporation, for the licensing of software programs for use for internal purposes only by employees at non-profit academic institutions of higher learning.

1.DEFINITIONS

1.1 The term Licensed Code shall mean the software entitled Pash, developed by Aleksandar Milosavljevic, Kenneth J. Kalafus and Andrew R. Jackson (collectively the Authors), employees of BAYLOR.

2.GRANT OF LICENSE

2.1 BAYLOR hereby grants to you a non-exclusive and non-transferable, right and license to use, modify, prepare derivative works of and execute solely for internal, research (non-commercial) purposes, the Licensed Code. This license shall be for use only on your computer (the Computer). The foregoing license does not include the right to copy the Licensed Code, or portions thereof, for any reason.

2.2 You acknowledge that the Licensed Code, including, but not limited to, all rights under federal copyright laws, are and shall remain at all times the exclusive property of BAYLOR. Any modifications or derivative works based on the Licensed Code are and shall be considered part of the Licensed Code and ownership thereof is retained by or vested in BAYLOR. You shall provide to BAYLOR reports of such modifications or derivative works and such modifications or derivative works shall be made available to BAYLOR upon receipt of a written request for such from BAYLOR.

2.3 You shall not distribute or transfer the Licensed Code to any other company, institution or person without the prior written permission of BAYLOR.

3.NO UPGRADES/NO SERVICE/DELIVERED AS IS

3.1 It is expressly understood and agreed that the Licensed Code and Manuals will be delivered to you on as "AS IS" basis as of the Agreement Date and that neither BAYLOR nor the Authors will be responsible for future support of the Licensed Code.

3.2 You acknowledge that you will not be entitled to any Licensed Code upgrades and that BAYLOR will not provide maintenance for the Licensed Code. If you find defects, bugs, in the Licensed Code, You shall notify BAYLOR of the existence of the bugs. Neither BAYLOR nor the Authors shall, however, have any obligation to fix any bugs in the Licensed Code.

4.DISCLAIMER OF WARRANTY

BAYLOR MAKES NO WARRANTIES OR REPRESENTATIONS, EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF FITNESS OR MERCHANTABILITY, REGARDING OR WITH RESPECT TO THE LICENSED CODE. BAYLOR MAKES NO WARRANTIES OR REPRESENTATIONS, EXPRESS OR IMPLIED, OF THE PATENTABILITY OR COPYRIGHTABILITY OF ANY OF THE LICENSED CODE OR OF THE ENFORCEABILITY OF ANY PATENTS OR COPYRIGHTS ISSUING THEREUPON, IF ANY, OR THAT THE LICENSED CODE, IS OR SHALL BE FREE FROM INFRINGEMENT OF ANY PATENT, COPYRIGHT OR OTHER RIGHTS OF THIRD PARTIES. BAYLOR MAKES NO WARRANTIES OR REPRESENTATIONS, EXPRESS OR IMPLIED, THAT THE LICENSED CODE SATISFIES REGULATORY REQUIREMENTS. YOU ACKNOWLEDGE THAT THE LICENSED CODE IS BEING LICENSED AS IS. BAYLOR HAS NOT TESTED THE LICENSED CODE FOR VIRUSES OR OTHER DEFECTS NOR HAS BAYLOR COMPLETED TESTING THE LICENSED CODE.

5.LIMITATION OF DAMAGES

BAYLOR shall not be liable for any monetary damages whatsoever with respect to your use of the Licensed Code nor shall BAYLOR be liable for any special, indirect, incidental or consequential damages arising out of or related to this Agreement, even if BAYLOR is advised of such damages.

6.INDEMNIFICATION

You will indemnify and hold BAYLOR, BAYLOR's trustees, officers, agents, employees, students, persons holding academic appointments within BAYLOR, and affiliated hospitals (the Indemnified parties) harmless from and against any and all claims, causes of action or lawsuits for personal injury (including death), property damage, and any other losses of any nature together with related expenses (including attorney's fees) made against the Indemnified parties resulting directly or indirectly from the use or possession of the Licensed Code by you, regardless of whether such claim, causes of action, lawsuits, other proceedings and the costs (including attorney's fees) related thereto result in whole or in part from the negligence of any of the Indemnified parties.

To obtain the Pash Package, please send an email to coarfa@bcm.edu with the following information:

  1. Your name
  2. Your institution
  3. Your email address (please indicate whether you would like to be added to our lab mailing list to receive information about Pash updates)
  4. A statement that you have read and agree to the License Agreement above
The Pash Package will then be sent to your email address as an attached file.


 

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