Phred Commercial License
Instructions for Licensing Phred

The Phred software is made available as part of the University of Washington’s Express Licensing program and commercial users are required to obtain this license in order to use. 
To complete the license, please:

  1. 1. REVIEW

    2. You will be directed to a page where you can review the license terms.

  2. 2. COMPLETE & SIGN

    3. To complete this agreement, you will be directed to a page to enter contact and site information.  In situations where contacts are the same individual, the information must be completed for each contact.     

  3. 3. PAYMENT

    4. Payment will be due at the time of signing in US Dollars (USD), and can be made by wire transfer, Check or Purchase Order (PO) per the payment option selected.  For payments made by wire transfer, there is an additional fee of $30 dollars USD.  If paying by wire transfer, Check or PO, an invoice will be sent to the invoicing contact as provided.  Payment must be received within 30 days of invoicing to retain access. 

  4. 4. ACCESS

    5. Upon receipt of payment, you will receive a confirmation and copy of the fully executed Agreement.  You will then be contacted by the UW to set up access. You will be contacted by email for access once the license has executed and payment is received.   

  5. 5. QUESTIONS

    6. Please contact our office if you have any questions about this process:

    Express Licensing Program               
    UW CoMotion
    University of Washington
    4545 Roosevelt Way NE, Suite 400
    Seattle, WA 98105-4608
    Email: license@uw.edu

    Non-Exclusive Software Site License Agreement
    Phred

    The University of Washington, a public institution of higher education and an agency of State of Washington, acting through UW CoMotion, Seattle, Washington (“UW”) and the undersigned Licensee  herein “Licensee” (individually “Party” or collectively “Parties”) agree as follows:

  6. 1. Background
  7. 1.1. UW desires to publish research codes in furtherance of its public interest mission.  Distribution of research codes is best facilitated by licensing a broad range of rights to industry to utilize these codes. Some of these codes were supported in part by the following grants: DOE DE-FG03-96ER62173 and NIH RO1 HG00774.
  8. 1.2. Licensee desires to obtain UW research software code and invest in the development, publication, validation and use of UW research software code at one or more of the Licensee’s sites.

  10. 2. Definitions
  11. 2.1. “Agreement” means this Non-Exclusive Software Site License Agreement.
  12. 2.2. “Annual License Fee” means the upfront fee and annual maintenance fee due by Licensee to UW under Section 6.
  13. 2.3. “Copyright” means the UW’s copyright in Software as ascribed in Sections 102 et seq. of the United States Copyright Act, amended from time to time, and International Treaty provisions, in effect from time to time, relating to the protection of copyrights worldwide.
  14. 2.4. “Effective Date” means the latest date upon which this Agreement is fully executed by both Parties.
  15. 2.5. “Licensing Contact” means the individual responsible for administering the financial terms of the Agreement and related correspondence from the UW. Licensee shall provide information on Licensing Contact.
  16. 2.6. “Modifications” means any changes or extensions introduced into the Software or otherwise based on or derived from the Software.  Modifications may include, but are not limited to, corrections of program errors, translations and stylistic restructuring of the Software, addition or deletion of functions or enhancement of existing functions of the Software, changes, or additions required to integrate the Software into other applications or to allow the Software to run under alternative operating systems or computer hardware configurations, and other adaptations of the Software. 
  17. 2.7. “Sites” means single street addresses, buildings, single campuses, or other single geographic locations at which the Software shall be maintained or used. License shall indicate the Sites authorized to use Software.
  18. 2.8. “Software” means the current release version of software code for Phred (as specified in Attachment A) for which Licensee desires to obtain a license.
  19. 2.9. “Technical Contact” means the individual authorized by Licensee to receive the Software and conduct all technical correspondence with UW. Licensee shall provide information on Technical Contact.

  21. 3. Grant
  22. 3.1. Grant of Rights in Copyright.  Commencing on the Effective Date, and provided that Licensee pays the Annual License Fee and conforms to the terms and conditions of this Agreement, UW hereby grants, and Licensee accepts, a limited, non-exclusive license under Copyright to use the Software at the Site(s), to modify the Software for use at the Site(s), and to make such copies of the Software in original or modified form as are necessary for use at the Site(s).  The license grant herein is limited to Licensee’s use at the Site(s) and does not authorize Software use by third parties at the Site or by anyone not located at the Site via the Internet or any other means.
  23. 3.2. No Licensee Ownership in Software. Licensee shall gain no ownership in the Software.  Licensee agrees not to allege or enjoin infringement or misappropriation by UW in any Software modifications, extensions, or other improvements prepared by UW, or by any third party obtaining Software modifications, extensions, or other improvements under license from UW.
  24. 3.3. Proprietary Markings. Licensee shall not remove or alter in the Software, or in any Modifications, the proprietary notices and legends as provided by UW, including without restriction any copyright, trademark, patent notices and legends pertaining to attribution, source of developments, funding sources, and disclaimer of risk.
  25. 3.4. Licensee Shall Not Distribute Software. Licensee shall not distribute, publish, or otherwise transfer or allow to be transferred the Software or any modified or unmodified copies thereof, in whole or in part, without prior written permission of UW.

  27. 4. Updates
  28. Provided that UW has received the Annual License Fee, UW will provide any updates to the Software that have been made based on UW-prepared Modifications on an “as available” basis during the term of this Agreement. If Licensee accepts these unofficial updates, such updates shall be covered under the terms of this Agreement.

  30. 5. Delivery
  31. Following execution of this Agreement and after UW has received the Annual License Fee, UW shall provide Licensee access to the Software by means of internet transmission (email and/or ftp).  Delivery is authorized by Licensee to be made to the Technical Contact.

  33. 6. Payment
  34. Licensee shall pay to UW the Annual License Fee of $2,500 USD for one (1) site. For 2-4 sites, the rate is discounted by 20% per site ($2,000 per site) and for 5 or more sites, the discount is 40% off a single site ($1,500 per site). Fees are due and payable upon execution of this Agreement. At each anniversary of the Effective Date, an Annual Maintenance Fee is due of $1,000 for a single site with discounts commensurate to those listed for multiple sites. Licensee shall indicate as part of execution of this Agreement the number of Sites for which the Software is licensed. Licensee shall be responsible for any charges, taxes and/or customs duties associated with payments made under this Agreement.

  36. 7. Term and Termination
  37. 7.1. Term.  This Agreement shall remain effective for the duration of the life of the copyright protection in the Software, or until terminated as set forth herein.
  38. 7.2. Termination by Licensee.  Licensee may terminate this Agreement at any time upon written notice to UW.  The termination shall be effective 30 days from date of notice.
  39. 7.3. Termination by UW.  UW may terminate this Agreement upon notice if Licensee is determined to be in material breach of this Agreement.  The termination shall be effective 30 days from the date of notice.  If the specified breach is cured before the effective date of termination, the Agreement shall not be terminated and the notice thereof shall have no effect.
  40. 7.4. No Limitation on Remedies. The provisions under which this Agreement may be terminated shall be in addition to any and all other legal remedies which either Party may have for the enforcement of any and all terms hereof, and do not in any way limit any other legal remedy such Party may have.
  41. 7.5. Effect of Termination. Termination of this Agreement will terminate all rights and licenses granted to Licensee relating to the Software.  Licensee shall certify in writing to UW within 10 days after termination that the Software, all copies made by Licensee during the term of this Agreement, and all Modifications thereof have been destroyed.

  43. 8. Disclaimers
  44. 8.1. Corporate Warranty.  Each Party represents and warrants to the other Party that it has full corporate power and authority to execute, deliver, and perform this Agreement, and that no other corporate proceedings by such Party are necessary to authorize the Party’s execution or delivery of this Agreement.
  45. 8.2. Software Provided “As-Is”.  The Software has been developed as part of research conducted at UW and is provided as a research courtesy.  The Software is experimental in nature and is available “AS IS,” without obligation by UW to provide Licensee services or support except as specified in this Agreement.  The entire risk as to the quality and performance of the Software is with Licensee.
  46. 8.3. General Disclaimer.  UW EXPRESSLY DISCLAIMS ANY AND ALL WARRANTIES, WHETHER EXPRESS OR IMPLIED, PERTAINING TO THE MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT OF THE SOFTWARE DISCLOSED OR ANY OTHER MATERIALS OTHERWISE PROVIDED TO LICENSEE UNDER THIS AGREEMENT.
  47. 8.4. Damages Cap.  Under no circumstances shall UW be liable in any lawsuit or other source of liability for more than payments received under this Agreement.

  49. 9. Indemnification
  50. Licensee shall indemnify and hold harmless UW, its regents, officers, employees, students, and agents against any and all claims, suits, losses, damages, costs, fees, and expenses resulting from Licensee’s possession and/or use of the Software, including but not limited to any damages, losses, or liabilities whatsoever with respect to death or injury to any person and damage to any property.  This indemnification clause shall survive the termination of this Agreement.

  52. 10. General
  53. 10.1. Governing Law, Venue.  This Agreement will be construed in accordance with, and its performance will be governed by, the laws of the State of Washington.  Any suit, action, or proceeding arising out of or relating to this Agreement will be decided in King County, Washington.  Licensee accepts the venue and jurisdiction of the Federal District Court of Washington, Seattle, or the King County Superior Courts and hereby waives any right to object to the governing law and venue provided herein.
  54. 10.2. No Waiver of Rights.  No omission or delay by either Party hereto in requiring due and punctual fulfillment of the obligations of any other Party hereto shall be deemed to constitute a waiver by such Party of its rights to require such due and punctual fulfillment, or of any other of its remedies hereunder.  Amendments to this Agreement must be in writing, reference this Agreement, and be signed by duly authorized representatives of UW and Licensee.
  55. 10.3. Enforceability.  If any provision of this Agreement shall be held to be invalid, illegal or unenforceable, the validity, legality, and enforceability of the remaining provisions will not be in any way affected or impaired thereby.
  56. 10.4. No Assignment.  This Agreement and the rights and benefits conferred upon Licensee hereunder may not be assigned or otherwise transferred by Licensee without the prior written consent of UW.
  57. 10.5. Force Majeure.  In the event either Party hereto is prevented from or delayed in the performance of any of its obligations hereunder by reason of acts of God, war, strikes, riots, storms, fires or any other cause whatsoever beyond the reasonable control of the non-performing Party, the non-performing Party shall be excused from the performance of any such obligation to the extent and during the period of such prevention or delay.
  58. 10.6. Entire Agreement, Construction.  This Agreement embodies the entire understanding of the Parties and supersedes all previous communications, representations, or understandings, either oral or written, between the Parties relating to the subject matter hereof.  Headings are provided for convenience only.
  59. 10.7. Use of Names. Licensee shall not use the name “University of Washington”, any abbreviation thereof, or any other means for identifying UW, or the names of any UW personnel or identifiers of the Software without prior written approval from UW, except as expressly authorized in this Agreement.

    60. Attachment A
    Software

    All platforms and formats are subject to change without notice.

    “Phred”:  A program that reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files. Source format only.