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Viral Genomics Software License: RC454

BROAD INSTITUTE
SOFTWARE LICENSE AGREEMENT
SINGLE USER LICENSE FOR
ACADEMIC AND 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 subscriber above (“LICENSEE”), and is effective at the date the downloading is completed and proper registration/licensee subscriber information submitted (“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 “BUG FIX(ES)” shall mean LICENSEE-created code that repairs a BROAD identified function of the PROGRAM.

1.2 “PROGRAM” shall mean copyright in the object code and source code known as RC454 (a.k.a. ReadClean454) 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 and 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.

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 the LICENSEE.

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. LICENSEE further agrees 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. LICENSEE further agrees not to reverse engineer or disassemble the PROGRAM code.

3. CONSIDERATION

In consideration of the licenses granted herein, LICENSEE agrees to provide a written evaluation of the PROGRAM including a description of its functionality or problems, areas for further improvement in the PROGRAM, and accurate registration information. LICENSEE hereby automatically grants to BROAD 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. LICENSEE further agrees to cite its use of the PROGRAM in any publication as follows: “Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, et al. (2012) Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection. PLoS Pathogens.”

4. 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, 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 2012 Broad Institute, Inc.
Notice of attribution: The RC454 (a.k.a ReadClean454) program was made available through the generosity of Genome Sequencing and Analysis Program 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 stated above for attribution purposes.

5. 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.

6. 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.

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.

AGREED this ___ day of ____, 2012


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LICENSEE