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TIminer
Copyright (c) 2016, Division of Bioinformatics, Innsbruck Medical University All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND C ONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 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.

NetMHCPan
Please obtain a NetMHCpan license at CBS and insert the download link for your NetMHCpan copy in the field below as proof for your registration

NetMHCpan url:

ACADEMIC SOFTWARE LICENSE AGREEMENT FOR END-USERS AT PUBLICLY FUNDED ACADEMIC, EDUCATION OR RESEARCH INSTITUTIONS FOR THE USE OF NetMHCpan 3.0 By downloading the Software you are consenting to be bound by and become a party to this agreement as the "Licensee". If you do not agree to all of the terms of this agreement, you must not click the Acceptance button, not install the product nor use the product, and you do not become a LICENSEE under this agreement. If you are not a member of a publicly funded Academic and/or Education and/or Research Institution you must obtain a commercial license, please send mail to (software@cbs.dtu.dk). This software license agreement is entered into by and between Center for Biological Sequence Analysis, Technical University of Denmark (hereinafter "CBS") and the "LICENSEE". WHEREAS CBS has the right to license all copyrights and other property rights in the Licensed Software identified as NetMHCpan 3.0 and developed by CBS and CBS desires to license the Software so that it becomes available for public use and benefit. WHEREAS LICENSEE is a public funded Academic and/or Education and/or Research Institution. WHEREAS LICENSEE desires to acquire a free non-exclusive license to use the Software for internal research purposes only. NOW, THEREFORE, in consideration of the mutual promises and covenants contained herein, the parties agree as follows: 1. Definitions "Licensed Software" means the specific version NetMHCpan 3.0 pursuant to this Agreement. Any opinion, findings, conclusions or recommendations expressed in the Licensed Software are those of the authors and do not necessarily reflect the views of CBS. 2. License Subject to the terms and conditions of this Agreement a non-exclusive, non-transferable License to use and copy the Licensed Software is made available free of charge for the LICENSEE which is a non-profit educational, academic and/or research institution. The License is only granted for personal and internal use in research only at one Site, where a Site is defined as a set of contiguous buildings in one location. The software will be used at only one location of LICENSEE. This license does not entitle Licensee to receive from CBS copies of the Licensed software on disks, tapes or CD's, hard-copy documentation, technical support, telephone assistance, or enhancements or updates to the Licensed Software. The user and any research assistants, co-workers or other workers who may use the Software agree to not give the program to third parties or grant licenses on software, which include the Software, alone or integrated into other software, to third parties. Modification of the source code is prohibited without the prior written consent of CBS. 3. Ownership Except as expressly licensed in this Agreement, CBS shall retain title to the Licensed Software, and any upgrades and modifications created by CBS. 4. Consideration In consideration for the license rights granted by CBS, LICENSEE will obtain this academic license free of charge. 5. Copies LICENSEE shall have the right to make copies of the Licensed Software for internal use at the Site and for back-up purposes under this Agreement, but agrees that all such copies shall contain the copyright notices and all other reasonable and appropriate proprietary markings or confidential legends that appear on the Licensed Software provided hereunder. 6. Support CBS shall have no obligation to offer support services to LICENSEE, and nothing contained herein shall be interpreted as to require CBS to provide maintenance, installation services, version updates, debugging, consultation or end-user support of any kind. 7. Software Protection LICENSEE acknowledges that the Licensed Software is proprietary to CBS. The software code shall be treated as trade secrets and confidential information of CBS, and LICENSEE agrees to use best efforts to hold the same in confidence. LICENSEE's obligation for confidentiality shall not extend to any information which is or becomes generally available to the public, is already known to or subsequently disclosed by third parties to LICENSEE and at its free disposal, or is independently developed by LICENSEE or its affiliates without the use of the confidential information disclosed by CBS, or is required by law or legal process. Except as other wise expressly permitted in this Agreement, Licensee my not (i) modify or create any derivative works of the Licensed Software or documentation, including customization, translation or localization; (ii) decompile, disassemble, reverse engineer, or otherwise attempt to derive the source code for the Product; (iii) redistribute, encumber, sell, rent, lease, sublicense, or otherwise transfer rights to the Licensed Software; (iv) remove or alter any trademark, logo, copyright or other proprietary notices, legends, symbols or labels in the Product; or (v) publish any results of benchmark tests run on the Product to a third party without CBS's prior written consent. 8. Representations of CBS to LICENSEE CBS represents to LICENSEE that (i) CBS has the right to grant the License and to enter into this agreement, (ii) that, to the best of CBS's knowledge, the Licensed software does not infringe any patent, copyright or trade secrets of any third party, provided however that such representation and warranty shall not apply to any addition to, or modifications or adaptation of, the Licensed Software made by LICENSEE and (iii) CBS undertakes to use best efforts to cooperate with and assist LICENSEE, at LICENSEE's expense, in defending itself against any action based on the alleged infringement of any third party patent, copyright or trade secret rights resulting from or relating to the use or licensing of the Licensed Software by LICENSEE. 9. Indemnity and Disclaimer of Warranties Except as expressly set forth in this agreement, CBS makes no representations or warranties, express or implied. The product is provided free of charge, and, therefore, on an "as is" basis, without warranty of any kind, express or implied, including without limitation the warranties that it is free of defects, virus free, able to operate on an uninterrupted basis, merchantable, fit for a particular purpose or non-interfering. The entire risk as to the quality and performance of the Licensed Software is borne by LICENSEE. By way of example, but not limitation, CBS makes no representations or warranties of merchantability or fitness for any particular application or, except as set forth in paragraph 8, that the use of the Software will not infringe any patents, copyrights or trademarks or other rights of third parties. The entire risk as to the quality and performance of the product is borne by LICENSEE. CBS shall not be liable for any liability or damages with respect to any claim by LICENSEE or any third party on account of, or arising from the license or use of the Software. Should the Licensed Software prove defective in any respect, LICENSEE and not LICENSOR or it's affiliates should assume the entire cost of any service and repair. This disclaimer of warranty constitutes an essential part of this agreement. No use of the licensed product is authorized hereunder except under this disclaimer. In no event will LICENSOR or its affiliates be liable for any indirect, special, incidental or consequential damages arising out of the use of or inability to use the product, including, without limitation, damages for lost profits, loss of goodwill, work stoppage, computer failure or malfunction, or any and all other commercial damages or losses, even if advised of the possibility thereof, and regardless of the legal or equitable theory (contract, tort or otherwise) upon which the claim is based. 10. Promotional Advertising & References LICENSEE may not use the name of the Licensed Software in its promotional advertising, product literature, and other similar promotional materials to be disseminated to the public or any portion thereof. LICENSEE agrees not to identify CBS in any promotional advertising or other promotional materials to be disseminated to the public, or any portion thereof without CBS's prior written consent. LICENSEE agrees that any reference to the software for crystallographic computations will cite one or more publications as set forth in the manual and in agreement with common scientific practice. CBS shall not use LICENSEE's name in publicity or advertising involving this Agreement or otherwise without LICENSEE's prior written consent which may be withheld at LICENSEE's sole discretion. 11. Term This Agreement and the license rights granted herein shall become effective as of the date this Agreement is executed by both parties and shall be perpetual unless terminated in accordance with this Section. CBS may terminate this Agreement at any time. Either party may terminate this Agreement at any time effective upon the other party's breach of any agreement, covenant, or representation made in this Agreement, such breach remaining uncorrected sixty (60) days after written notice thereof. LICENSEE shall have the right, at any time, to terminate this Agreement without cause by written notice to CBS specifying the date of termination. Upon termination, LICENSEE shall destroy all full and partial copies of the Licensed Software. 12. Governing Law This Agreement shall be construed in accordance with the laws of Denmark. 13. General The parties agree that this Agreement is the complete and exclusive agreement among the parties and supersedes all proposals and prior agreements whether written or oral, and all other communications among the parties relating to the subject matter of this Agreement. This Agreement cannot be modified except in writing and signed by both parties. Failure by either party at any time to enforce any of the provisions of this Agreement shall not constitute a waiver by such party of such provision nor in any way affect the validity of this Agreement. The invalidity of singular provisions does not affect the validity of the entire understanding. The parties are obligated, however, to replace the invalid provisions by a regulation which comes closest to the economic intent of the invalid provision. The same shall apply mutatis mutandis in case of a gap. IN WITNESS WHEREOF, the LICENSEE hereto have caused this Agreement to be duly executed on the date of the download of the software and by accepting the license conditions by pressing the Acceptance button.

Kallisto
Copyright ©2015. The Regents of the University of California (Regents). All Rights Reserved. Permission to use, copy, modify, and distribute this software and its documentation for educational and research not-for-profit purposes, without fee and without a signed licensing agreement, is hereby granted, provided that the above copyright notice, this paragraph and the following two paragraphs appear in all copies, modifications, and distributions. Contact The Office of Technology Licensing, UC Berkeley, 2150 Shattuck Avenue, Suite 510, Berkeley, CA 94720-1620, (510) 643-7201, for commercial licensing opportunities. Created by Nicolas Bray, Harold Pimentel, Pall Melsted and Lior Pachter, University of California, Berkeley IN NO EVENT SHALL REGENTS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF REGENTS HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". REGENTS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.

GATK
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 415 Main Street, 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 GATK3 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute.org/gatk 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. PHONE-HOME FEATURE LICENSEE expressly acknowledges that the PROGRAM contains an embedded automatic reporting system (“PHONE-HOME”) which is enabled by default upon download. Unless LICENSEE requests disablement of PHONE-HOME, LICENSEE agrees that BROAD may collect limited information transmitted by PHONE-HOME regarding LICENSEE and its use of the PROGRAM. Such information shall include LICENSEE’S user identification, version number of the PROGRAM and tools being run, mode of analysis employed, and any error reports generated during run-time. Collection of such information is used by BROAD solely to monitor usage rates, fulfill reporting requirements to BROAD funding agencies, drive improvements to the PROGRAM, and facilitate adjustments to PROGRAM-related documentation. 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. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication. Copyright 2012-2016 Broad Institute, Inc. Notice of attribution: The GATK3 program was made available through the generosity of Medical and Population Genetics 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 states 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, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4. 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 he Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.

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