ATHLATES Academic Software License

SOFTWARE LICENSE AGREEMENT
SINGLE USER LICENSE FOR
ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY

By downloading the PROGRAM as defined below you agree to the following terms.

This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (“BROAD”) and the subscriber above (“LICENSEE”), and is effective at the date the downloading is completed and proper registration/licensee subscriber information submitted (“EFFECTIVE DATE”). Under this Agreement, BROAD (a) represents BROAD ownership interests in the PROGRAM and (b) acts as the sole and exclusive agent for and on behalf of joint PROGRAM owner The Washington University, a corporation established by special act of the Missouri General Assembly approved February 22, 1853 and acts amendatory thereto, having its principal offices at One Brookings Drive, St. Louis, Missouri 63130 (“WASH U”; together with BROAD, “LICENSORS”).

WHEREAS, LICENSEE desires to license the PROGRAM and BROAD and WASH U wish 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 and WASH U desire 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 “BUG FIX(ES)” shall mean LICENSEE-created code that repairs a function of the PROGRAM identified by BROAD and/or WASH U.
1.2 “PROGRAM” shall mean the object code and source code in which BROAD and WASH U hold rights, including copyrights, under the software application known as ATHLATES v1.0 (BROAD case ref. #BI-2012/008; WASH U case ref. #013332) and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org on the EFFECTIVE DATE.

2. LICENSE
2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for a single user and solely for academic noncommercial 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 as necessary for academic noncommercial research purposes.
2.2 No Sublicensing or Additional Rights. In no event shall LICENSEE sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE agrees not to put the PROGRAM on a network, server, or other similar technology that may be accessed by any individual other than those employed by the LICENSEE who require access to the PROGRAM to conduct academic noncommercial research.
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, WASH U 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 a service. LICENSEE further agrees:

(a) that the PROGRAM shall not be rewritten in another computer language or otherwise adapted to circumvent the need for obtaining a license for use of the PROGRAM; and
(b) not to reverse engineer or disassemble the PROGRAM code; and
(c) not to use the PROGRAM for research that is supported by, funded by, or performed on behalf of for-profit or commercial enterprise or that may otherwise obligate intellectual property rights to a for-profit or commercial enterprise.

3. CONSIDERATION
In consideration of the licenses granted herein, LICENSEE hereby:

(a) grants to BROAD and WASH U a non-exclusive, royalty-free, irrevocable worldwide license to any LICENSEE BUG FIXES or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute; such modifications and BUG FIXES shall be provided to BROAD promptly upon their creation; and
(b) agrees to provide BROAD accurate registration information; and
(c) agrees, upon request from BROAD, a written evaluation of the PROGRAM including a description of its functionality or problems, areas for further improvement in the PROGRAM; and
(d) LICENSEE further agrees to cite its use of the PROGRAM in any publication as follows:
C. Liu, X. Yang, B. Duffy, T. Mohanakumar, R.D. Mitra, M.C. Zody, J.D. Pfeifer (2012) “ATHLATES: accurate typing of human leukocyte antigen through exome sequencing” Nucl. Acids Res. (2013) [doi: 10.1093/nar/gkt481].

4. OWNERSHIP OF INTELLECTUAL PROPERTY
LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD and WASH U. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies, and on modifications and BUG FIXES where applicable. LICENSEE shall be entitled to establish all proprietary rights for itself in the modifications or BUG FIXES created pursuant to Section 2.1, whether in the nature of trade secrets or copyrights, provided that all such rights are subject to BROAD’s copyright and that any copyright registration by LICENSEE gives full attribution to BROAD’s copyright. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication:

Copyright 2013 Broad Institute, Inc. and Washington University. ATHLATES is made available through the generosity of the Broad Institute, Inc. and Washington University. For details see: http://www.broadinstitute.org.

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 stated above for attribution purposes.

5. INDEMNIFICATION
LICENSEE shall indemnify, defend, and hold harmless LICENSORS, 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.

6. NO REPRESENTATIONS OR WARRANTIES
THE PROGRAM IS PROVIDED BY THE BROAD "AS IS." LICENSORS MAKE 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 LICENSORS OR THEIR RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY, 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 REGARDLESS OF WHETHER LICENSORS SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.

7. 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.

8. MISCELLANEOUS
8.1 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.
8.2 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.
8.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 4, 5, 6 and Sections 2.2, 2.3, 8.3, and 8.4.
8.4 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.
8.5 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.
8.6 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.
8.7 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.