By downloading the PROGRAM you agree to the following terms of use:

BROAD INSTITUTE SOFTWARE LICENSE AGREEMENT
FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY

This Agreement is made between the Broad Institute, Inc. with a principal 
address at 7 Cambridge Center, Cambridge, MA 02142 ("BROAD") and the 
LICENSEE and is effective at the date the downloading is completed 
("EFFECTIVE DATE").
WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, 
and BROAD wishes to have this PROGRAM utilized in the public interest, 
subject only to the royalty-free, nonexclusive, nontransferable license 
rights of the United States Government pursuant to 48 CFR 52.227-14; and
WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant 
a license on the following terms and conditions.
NOW, THEREFORE, in consideration of the promises and covenants made herein, 
the parties hereto agree as follows:

1. DEFINITIONS
1.1	"PROGRAM" shall mean copyright in the object code and source code 
known as MutSig and related documentation, if any, as they exist on the 
EFFECTIVE DATE and can be downloaded from 
http://www.broadinstitute.org/cancer/cga/MutSig on the EFFECTIVE DATE.

2. LICENSE
2.1   Grant. Subject to the terms of this Agreement, BROAD hereby grants to 
LICENSEE, solely for academic non-commercial research purposes, a non-
exclusive, non-transferable license to: (a) download, execute and display 
the PROGRAM and (b) create bug fixes and modify the PROGRAM. 

LICENSEE hereby automatically grants to BROAD a non-exclusive, royalty-
free, irrevocable license to any LICENSEE bug fixes or modifications to the 
PROGRAM with unlimited rights to sublicense and/or distribute.  LICENSEE 
agrees to provide any such modifications and bug fixes to BROAD promptly 
upon their creation.

The LICENSEE may apply the PROGRAM in a pipeline to data owned by users 
other than the LICENSEE and provide these users the results of the PROGRAM 
provided LICENSEE does so for academic non-commercial purposes only.  For 
clarification purposes, academic sponsored research is not a commercial use 
under the terms of this Agreement.

2.2  No Sublicensing or Additional Rights. LICENSEE shall not sublicense or 
distribute the PROGRAM, in whole or in part, without prior written 
permission from BROAD.  LICENSEE shall ensure that all of its users agree 
to the terms of this Agreement.  LICENSEE further agrees that it shall not 
put the PROGRAM on a network, server, or other similar technology that may 
be accessed by anyone other than the LICENSEE and its employees and users 
who have agreed to the terms of this agreement.

2.3  License Limitations. Nothing in this Agreement shall be construed to 
confer any rights upon LICENSEE by implication, estoppel, or otherwise to 
any computer software, trademark, intellectual property, or patent rights 
of BROAD, or of any other entity, except as expressly granted herein. 
LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for 
any commercial purpose, including without limitation, as the basis of a 
commercial software or hardware product or to provide services. LICENSEE 
further agrees that the PROGRAM shall not be copied or otherwise adapted in 
order to circumvent the need for obtaining a license for use of the 
PROGRAM.  

3. OWNERSHIP OF INTELLECTUAL PROPERTY 
LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. 
The PROGRAM is marked with the following BROAD copyright notice and notice 
of attribution to contributors. LICENSEE shall retain such notice on all 
copies.  LICENSEE agrees to include appropriate attribution if any results 
obtained from use of the PROGRAM are included in any publication.

Copyright 2012 Broad Institute, Inc.
Notice of attribution:  The MutSig program was made available through the 
generosity of the Cancer Genome Analysis group at the Broad Institute, Inc. 

LICENSEE shall not use any trademark or trade name of BROAD, or any 
variation, adaptation, or abbreviation, of such marks or trade names, or 
any names of officers, faculty, students, employees, or agents of BROAD 
except as states above for attribution purposes.

4. INDEMNIFICATION
LICENSEE shall indemnify, defend, and hold harmless BROAD, and their 
respective officers, faculty, students, employees, associated investigators 
and agents, and their respective successors, heirs and assigns, 
("Indemnitees"), against any liability, damage, loss, or expense (including 
reasonable attorneys fees and expenses) incurred by or imposed upon any of 
the Indemnitees in connection with any claims, suits, actions, demands or 
judgments arising out of any theory of liability (including, without 
limitation, actions in the form of tort, warranty, or strict liability and 
regardless of whether such action has any factual basis) pursuant to any 
right or license granted under this Agreement.

5. NO REPRESENTATIONS OR WARRANTIES
THE PROGRAM IS DELIVERED "AS IS."  BROAD MAKES NO REPRESENTATIONS OR 
WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR 
IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, 
FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT 
OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES 
OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER 
LITERATURE MAY BE ISSUED FROM TIME TO TIME.
IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, 
AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR 
CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC 
DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD 
SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF 
THE POSSIBILITY OF THE FOREGOING.

6. ASSIGNMENT
This Agreement is personal to LICENSEE and any rights or obligations 
assigned by LICENSEE without the prior written consent of BROAD shall be 
null and void.

7. MISCELLANEOUS
7.1 Export Control. LICENSEE gives assurance that it will comply with all 
United States export control laws and regulations controlling the export of 
the PROGRAM, including, without limitation, all Export Administration 
Regulations of the United States Department of Commerce. Among other 
things, these laws and regulations prohibit, or require a license for, the 
export of certain types of software to specified countries.
7.2 Termination. LICENSEE shall have the right to terminate this Agreement 
for any reason upon prior written notice to BROAD. If LICENSEE breaches any 
provision hereunder, and fails to cure such breach within thirty (30) days, 
BROAD may terminate this Agreement immediately. Upon termination, LICENSEE 
shall provide BROAD with written assurance that the original and all copies 
of the PROGRAM have been destroyed, except that, upon prior written 
authorization from BROAD, LICENSEE may retain a copy for archive purposes.
7.3 Survival. The following provisions shall survive the expiration or 
termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 
7.3, and 7.4.
7.4 Notice. Any notices under this Agreement shall be in writing, shall 
specifically refer to this Agreement, and shall be sent by hand, recognized 
national overnight courier, confirmed facsimile transmission, confirmed 
electronic mail, or registered or certified mail, postage prepaid, return 
receipt requested.  All notices under this Agreement shall be deemed 
effective upon receipt. 
7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, 
supplemented, or otherwise modified only by means of a written instrument 
signed by all parties. Any waiver of any rights or failure to act in a 
specific instance shall relate only to such instance and shall not be 
construed as an agreement to waive any rights or fail to act in any other 
instance, whether or not similar. This Agreement constitutes the entire 
agreement among the parties with respect to its subject matter and 
supersedes prior agreements or understandings between the parties relating 
to its subject matter. 
7.6 Binding Effect; Headings. This Agreement shall be binding upon and 
inure to the benefit of the parties and their respective permitted 
successors and assigns. All headings are for convenience only and shall not 
affect the meaning of any provision of this Agreement.
7.7 Governing Law. This Agreement shall be construed, governed, interpreted 
and applied in accordance with the internal laws of the Commonwealth of 
Massachusetts, U.S.A., without regard to conflict of laws principles.



