End User License Agreement for SeqGeq

SeqGeq End-User License Agreement (EULA)

1. Introduction and Acceptance. This License Agreement is a legal agreement among You as an individual (the “You”, or “Your”), the institution paying for this license (the “Purchaser”), and FlowJo, LLC (“FlowJo”) (referred to as “We”, “Us”, or “Our”, as applicable) regarding the use of SeqGeq® software, which includes user documentation provided in electronic form and access to database information (together, the “Software”).

BEFORE YOU ACCEPT THIS AGREEMENT, ON YOUR OWN BEHALF AND ON BEHALF OF THE PURCHASER, CAREFULLY READ ITS TERMS AND CONDITIONS. BY CHECKING THE “I ACCEPT” BOX OF THIS AGREEMENT, YOU ARE AGREEING TO BE BOUND BY AND ARE BECOMING A PARTY TO THIS AGREEMENT. IF YOU DO NOT AGREE TO ALL OF THE TERMS AND CONDITIONS OF THIS AGREEMENT, PLEASE MAKE NO USE OF THE SOFTWARE AND DESTROY OR DELETE ANY COPIES IN YOUR POSSESSION.

YOU ACKNOWLEDGE THAT YOU HAVE READ AND UNDERSTAND THE TERMS OF THIS AGREEMENT, ESPECIALLY SECTION 7 (WHICH DISCLAIMS THAT ANY WARRANTIES ARE PROVIDED TO YOU), AND SECTION 8 (WHICH LIMITS THE LIABILITY OF FLOWJO AND OTHERS TO YOU).

2. Grant of License. Subject to the restrictions and the other terms and conditions set forth below, this Agreement grants you a limited, non-exclusive, non-transferable, non-sublicensable, revocable license during the term of this Agreement to register, install and use one copy of the specified version of the Software, in object-code form only. This is an individual license only for You and may not be transferred to any person or entity or used by any other person or entity.

3. Ownership. The license granted under this Agreement does not constitute a transfer or sale of any ownership rights in the Software. Except for the limited non-exclusive license granted in Paragraph 2 above, as between You and FlowJo, FlowJo owns all right, title and interest in the Software. The Software is protected by applicable intellectual property laws, including United States copyright laws and international treaties.

4. License Restrictions. You may not: (i) copy, reverse engineer, decompile, or disassemble the Software or attempt to derive the source code of the Software, (ii) remove or destroy any of the Software’s copyright notices, trademark notices or other proprietary markings, (iii) modify or adapt the Software, merge the Software into another program or create derivative works based on the Software, (iv) transfer the Software or any of Your rights or obligations under this Agreement, (v) install, copy or use the Software on a virtual machine, (vi) permit any person or entity other than You to use the Software, (vii) use the Software in concurrent sessions, (viii) concurrently use more than one instance of the Software or have concurrent uses of command-line instances, (ix) export or re-export the Software, or (x) use a terminal server to share a license, even if use is non-concurrent. You acknowledge and agree the Software is confidential and proprietary information of FlowJo. You agree not to copy, disseminate or otherwise provide the Software to any other person or entity. YOU FURTHER ACKNOWLEDGE THAT IT IS YOUR RESPONSIBILITY TO VALIDATE THE SOFTWARE AS PART OF YOUR ASSAY AND USE IT IN A MANNER COMPLIANT WITH ITS INTENDED USE AND WITH APPLICABLE RULES AND REGULATIONS AND ANY AND ALL DIRECTIONS FOR USE INCLUDED WITH THE PURCHASE OF THE SOFTWARE.

You are solely responsible for maintaining adequate security, protection and backup for the device(s) on which the Software is installed, and your use of the Software.

5) Data

“Data” includes all information, files, or data (including personally identifiable data) uploaded to, provided to, stored on, created within, created as a result of use of FlowJo, including without limitation, any genomic information generated by sequencing instruments and further analysis or processing conducted on such information.

5A. Usage Data. FlowJo may collect and process Usage Data in connection with the usage of the Software. “Usage Data” means Data related to user’s use of the Software, including without limitation, IP address, Mac address, browser type and version, operating system and interface, version of SeqGeq, underlying license information, date and time of SeqGeq usage. FlowJo agrees it will use Usage Data only for FlowJo’s business purposes and for research and development purposes. FlowJo shall own all right, title and interest in and to Usage Data. You hereby grant FLOWJO and its affiliates a non-exclusive, worldwide, royalty-free, perpetual, irrevocable, and transferable right to create derivative works based on, distribute, perform, display, use, or in any way exploit any such Usage Data.

5B. No Third Party Personal Data. You agree that you will not provide any personally identifying information or personal information or personal data as defined by applicable law (e.g, HIPAA, EU General Data Protection Regulation) relating to any third parties, in particular relating to patients. For example, you will not provide the name, date of birth, address, social security, government issued identification number, or any other information that could directly or indirectly identify the individual from whom any genomic or other information was derived.

5C. Security of data. While we use industry standard security, no system can perfectly guard against risks of intentional or inadvertent disclosure of Data. When using FlowJo, Data will be transmitted over a medium that is beyond the control of FlowJo. You expressly assume the sole risk of any unauthorized disclosure or intentional intrusion, or of any delay, failure, loss, interruption or corruption of Data or other information transmitted in connection with the use of FlowJo.

5D. How We Protect and Use Your Personal Data. The FlowJo Privacy Policy applies to You, the Purchaser, and Your Data with respect to FlowJo.

6. Termination. This Agreement will commence upon Your acceptance of this Agreement. Your right to use the Software will terminate immediately upon the earlier of: i) Your failure to comply with any term or condition of this Agreement; or ii) Your return, destruction or deletion of all copies of the Software in your possession, custody or control. Upon termination of this Agreement for any reason, you agree to immediately cease any use of the Software, you agree to immediately return to FlowJo or delete or destroy all copies of the Software in your possession, custody or control, and You will certify in writing to FlowJo that all copies of the Software have either been returned to FlowJo or otherwise destroyed or deleted. FlowJo’s rights and Your obligations will survive the termination of this Agreement.

FLOWJO may change, or discontinue the Software at any time, including the availability of any feature, database, or content.

7. No Warranty or Maintenance. THE SOFTWARE IS PROVIDED “AS IS.” FLOWJO MAKES NO REPRESENTATIONS OR WARRANTIES WITH RESPECT TO THE SOFTWARE, WHETHER EXPRESSED, IMPLIED, STATUTORY, OR OTHERWISE, AND FLOWJO SPECIFICALLY DISCLAIMS ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS, NON-INFRINGEMENT OR OTHERWISE. FLOWJO HAS NO OBLIGATION TO PROVIDE MAINTENANCE OF THE SOFTWARE. ANY MAINTENANCE OF THE SOFTWARE BY FLOWJO SHALL BE SUBJECT TO A SEPARATE WRITTEN AGREEMENT BETWEEN YOU AND FLOWJO.

8. Liability Limitation. IN NO EVENT WILL FLOWJO BE LIABLE FOR ANY CONSEQUENTIAL, SPECIAL, INDIRECT, INCIDENTAL, OR PUNITIVE DAMAGES WHATSOEVER (INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION, LOSS OF DATA OR OTHER SUCH PECUNIARY LOSS) ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE, EVEN IF FLOWJO HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. IN NO CASE WILL FLOWJO’S AGGREGATE LIABILITY ARISING OUT OF THIS AGREEMENT AND/OR YOUR USE OF THE SOFTWARE EXCEED THE FEES ACTUALLY PAID BY YOU FOR YOUR USE OF THE SOFTWARE UNDER THIS AGREEMENT.

9. Prohibited Uses, Indemnification. The Software has not been approved as a medical device by the United States Food and Drug Administration and as such is not marketed with any claims concerning the performance of the Software for use in interpreting data for the clinical diagnosis or treatment of any disease, disorder or other medical condition. Neither the Software nor any data derived from use of the Software shall be used, directly or indirectly, for the clinical diagnosis or treatment of any disease, disorder or other medical condition. You will indemnify, defend and hold harmless FlowJo, its officers, directors, shareholders, members, managers, employees, agents, representatives, successors and assigns, from and against any and all claims, lawsuits, actions and demands arising out of or related in any way to use of the Software in any manner not expressly authorized by this Agreement, including without limitation use of the Software or any data derived from use of the Software to perform any analysis classified as an Analyte Specific Reagent medical test or any clinical diagnosis or treatment of any disease, disorder or other medical condition. Your indemnification obligations shall include, but not be limited to, all costs of defense, including all attorney fees and expenses of counsel, any and all judgments and other amounts assessed by the court or other government body, and any and all other expenses and costs incurred as a result of any such lawsuit, action, demand or claim.

To the fullest extent allowed by law, you will indemnify and hold FLOWJO and FLOWJO Parties harmless from all damages, liabilities, settlements, expenses, fines, penalties, expenses, costs and attorneys’ fees arising from or related to any claim or demand made by any third party due to or arising out of 1) your use of the software, 2) or the infringement by you (or any third party using your account) of any intellectual property or other right of any person or entity.

10. Modifications to this Agreement. We reserve the right to change this EULA at any time. When we make changes, we will post the changed EULA at http://www.flowjo.com/flowjo-eula/ and it will become effective thirty days thereafter ("Effective Date"). The changed EULA supersedes and replaces the prior version. Your continued access to or use of one or more of the Services and/or data derived therefrom shall constitute your acceptance of such changed EULA. For the avoidance of doubt and unless expressly stated otherwise in this EULA, the changed EULA applies to all uses of the Services, including all User Information and information about the Data, inclusive of aggregation of Data, both before and after the Effective Date.

11. Trademarks. SeqGeq® is a registered trademark owned by FlowJo. Certain of the product and FlowJo names used in this Agreement, the Software and/or the documentation may constitute trademarks. You are not authorized to use any such trademarks.

12. General. This Agreement sets forth the entire agreement between You, the Purchaser, and FlowJo with respect to the Software. This Agreement shall be construed, interpreted, and governed by the laws of the state of Oregon, without reference to its conflict-of-laws principles. Any action between You and FlowJo regarding this Agreement and/or Your use of the Software will be subject to the exclusive jurisdiction of the courts of the State of Oregon. If any provision of this Agreement is held invalid or unenforceable, the remainder of this Agreement will continue in full force and effect.

13. Miscellaneous. The failure of any party to exercise, in any respect, any right provided for herein shall not be deemed a waiver of any further rights hereunder. FLOWJO shall not be liable for any failure to perform its obligations hereunder where such failure results from any cause beyond FLOWJO's reasonable control. If any provision of this Agreement is found to be unenforceable or invalid, that provision shall be limited or eliminated to the minimum extent necessary so that this Agreement shall otherwise remain in full force and effect and enforceable. This Agreement is not assignable, transferable or sublicensable by you except with FLOWJO’s prior written consent. FLOWJO may transfer, assign or delegate this Agreement and its rights and obligations without consent. Both parties agree that this Agreement is the complete and exclusive statement of the mutual understanding of the parties and supersedes and cancels all previous written and oral agreements, communications and other understandings relating to the subject matter of this Agreement, and that all modifications must be in a writing signed by both parties, except as otherwise provided herein. No agency, partnership, joint venture, or employment is created as a result of this Agreement and you do not have any authority of any kind to bind FLOWJO in any respect whatsoever.

14. Questions. Should you have any questions concerning this Agreement, or if you desire to contact FlowJo for any reason, please contact: techsupport@flowjo.com.

15. Third Party Software and Licenses. FlowJo makes use of third party libraries. This section 15 lists in full those third-party libraries. Where source was modified, it can be obtained from FlowJo, LLC by request. If you cannot resolve the general license pointers below, i.e., “GNU LGPLv2.1″ using a web search, please contact us and we will help you find it. t-SNE is Copyright (c) 2014, Laurens van der Maaten (Delft University of Technology). All rights reserved.

This software makes use of the following libraries under the Apache 2.0 license:

Xerces XML-Commons APIs http://xerces.apache.org/xerces2-j/

Ant http://ant.apache.org/

Apache Batik http://xmlgraphics.apache.org/batik/

Apache Commons Codec http://commons.apache.org/proper/commons-codec/

Apache Commons Logging http://commons.apache.org/proper/commons-logging/

Apache Poi: API for MS documents http://poi.apache.org/

HC Fluent http://hc.apache.org/httpcomponents-client-4.3.x/

HttpAsyncClient http://hc.apache.org/httpcomponents-asyncclient-4.0.x/

HttpComponents http://hc.apache.org/httpcomponents-client-4.3.x/

HttpComponents http://hc.apache.org/httpcomponents-core-ga/

JH Labs Java Image Processing http://www.jhlabs.com/ip/filters/download.html

Xerces XML-Commons APIs http://xerces.apache.org/xerces2-j/

This software makes use of the following libraries under the BSD license:

Flamingo http://java.net/projects/flamingo/

JavaGraphics (bric) https://java.net/projects/javagraphics

This software makes use of the Timing Framework library http://java.net/projects/timingframework under the BSD2 and Apache 2.0 license.

This software makes use of the Proxy Vole - Network proxy detection library https://code.google.com/p/proxy-vole/libraries under the BSD3 license.

This software makes use of the following libraries under the BSD2 license:

Animated Transitions http://java.net/projects/animatedtransitions/

Transition Tabbed Pane http://java.net/projects/javagraphics

Trident Java Animation Library http://kenai.com/projects/trident/pages/Home

This software makes use of the JUnit library http://junit.org/ under the Common Public License (CPL).

This software makes use of the Standard Widget Toolkit library http://www.eclipse.org/swt/ under the Eclipse Public License (EPL).

This software makes use of the Vecmath library http://java.net/projects/vecmath/ under the GNU General Public License (GPL).

This software makes use of the following libraries under the Java 3D license:

Java 3D Core http://www.oracle.com/technetwork/java/javase/tech/index-jsp-138252.html

Java 3D Utils http://www.oracle.com/technetwork/java/javase/tech/index-jsp-138252.html

This software makes use of the Javax Servlet http://www.oracle.com/technetwork/java/javaee/downloads/index.html under the JDK 6 license.

This software makes use of the following libraries under the Lesser General Public License (LGPL):

DJNative Swing http://djproject.sourceforge.net/ns/

DJNative Swing SWT http://djproject.sourceforge.net/ns/

FreeHEP export http://java.freehep.org/

FreeHEP graphics2d http://java.freehep.org/

FreeHEP graphicsio http://java.freehep.org/

FreeHEP graphicsio PDF http://java.freehep.org/

FreeHEP graphicsio SVG http://java.freehep.org/

FreeHEP io http://java.freehep.org/

FreeHEP java3d http://java.freehep.org/

FreeHEP util http://java.freehep.org/

FreeHEP xml http://java.freehep.org/

JNA http://jna.java.net/

JNA Window Utils http://jna.java.net/javadoc/platform/com/sun/jna/platform/WindowUtils.html

This software makes use of the following under the Massachusetts Institute of Technology (MIT) License:
AlphanumComparator from http://www.davekoelle.com/files/AlphanumComparator.java used for sorting p-value and fold-change statistics

This software makes use of the following libraries under the Lesser General Public License (LGPL) 2.1:

SwingX http://swingx.java.net/ LGPL 2.1

This software makes use of the Quaqua Look and Feel http://www.randelshofer.ch/quaqua/library under the Lesser General Public License (LGPL) and/or BSD license.

This software makes use of the following libraries under the Mozilla Public License (MPL):

Mozilla Interfaces (XULRunner) https://developer.mozilla.org/en-US/docs/XULRunner

Mozilla Rhino https://developer.mozilla.org/en-US/docs/Mozilla/Projects/RhinoMozilla Rhino https://developer.mozilla.org/en-US/docs/Mozilla/Projects/Rhino

This software makes use of the following libraries which are in the Public Domain:

ImageJ http://imagej.nih.gov/ij/

JAMA matrix package http://math.nist.gov/javanumerics/jama/

This software makes use of the following libraries, for which we have satisfied their specific license requirements

WMFWriter http://piet.jonas.com/WMFWriter/WMFWriter.html

Apple Java Extensions http://developer.apple.com/library/mac/#/legacy/mac/library/samplecode/AppleJavaExtensions/Introduction/Intro.html#//apple_ref/doc/uid/DTS10000677-Intro-DontLinkElementID_2

Chernoff Faces https://github.com/wiseman/chernoff-faces

JSON http://www.json.org/java/index.html

SpringUtilities http://docs.oracle.com/javase/tutorial/uiswing/examples/layout/SpringGridProject/src/layout/SpringUtilities.java

This software makes use of the Stanford Transformation library provided by Wayne Moore.

This software makes use of code modules from:

Laurens Van Der Matten and includes the following notice:

*** tSNE ***

L.J.P. van der Maaten. Accelerating t-SNE using Tree-Based Algorithms. Journal of Machine Learning Research 15(Oct):3221-3245, 2014.

L.J.P. van der Maaten and G.E. Hinton. Visualizing Non-Metric Similarities in Multiple Maps. Machine Learning 87(1):33-55, 2012.

L.J.P. van der Maaten. Learning a Parametric Embedding by Preserving Local Structure. In Proceedings of the Twelfth International Conference on Artificial Intelligence & Statistics (AI-STATS), JMLR W&CP 5:384-391, 2009.

L.J.P. van der Maaten and G.E. Hinton. Visualizing High-Dimensional Data Using t-SNE. Journal of Machine Learning Research 9(Nov):2579-2605, 2008.

*** Cell Ontology ***

Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH,Brinkman RR. flowCL: ontology-based cell population labelling in flow cytometry. Bioinformatics. 2015 Apr 15;31(8):1337-9. doi: 10.1093/bioinformatics/btu807. Epub 2014 Dec 6.

*** FlowMeans ***

Aghaeepour N, Nikolic R, Hoos HH, Brinkman RR. Rapid cell population identification in flow cytometry data. Cytometry A. 2011 Jan;79(1):6-13. doi: 10.1002/cyto.a.21007.

*** SPADE ***

Peng Qiu, Erin F. Simonds, Sean C. Bendall, Kenneth D. Gibbs Jr., Robert V. Bruggner, Michael D. Linderman, Karen Sachs, Garry P. Nolan, Sylvia K. Plevritis, "Extracting a Cellular Hierarchy from High-dimensional Cytometry Data with SPADE", Nature Biotechnology, 2011.

*** R ***

R Core Team (2015). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/

*** Eigen ***
Eigen may be obtained from http://eigen.tuxfamily.org
Eigen is licensed under the MPL2 license: https://www.mozilla.org/en-US/MPL/2.0/
Eigen modifications incorporated in this software are available upon request; please email seqgeqsupport@bd.com

You will not and will not allow anyone else to reverse engineer, decompile, disassemble, translate, modify, adapt, or enhance such Software or create any derivative works of such Software, or extract ideas, algorithms, procedures, workflows, or system architecture from such Software. You will not remove, obscure, or alter any proprietary rights notices (including copyright and trademark notices) that may be affixed to or contained within the Software. Some Software may be provided by a third party and that third party may require you to agree to terms of use or license terms applicable to their software. You must agree to such terms of use or license in order to use such third-party Software. Some of the Software may be offered under an open source license. There may be provisions in such open source license that expressly override some of the terms of this Agreement. If that is the case, only those terms of this Agreement that are in conflict with the open source license will be overridden.