exercise cfChIP-seq

cfChIP exercise

DATA ACCESS AGREEMENT This DATA ACCESS AGREEMENT (this “Agreement”) made and entered into on _________201_ between the Hebrew University of Jerusalem, the Authority for R&D, Edmond J. Safra Campus, Jerusalem 91390, Israel (the "Provider Institution"), on behalf of Prof. Nir Friedman (the “Provider Scientist”); and between __________________with offices at ____________ (the “User Institution”) on behalf of Prof./Dr._______________ (the “User”), relating to the access by the User of certain data deposited by the Provider Scientist at the European Genome-phenome Archive (“EGA”) for use in a study. These terms and conditions govern access to the managed access datasets (details of which are set out in Appendix I) to which the User Institution has requested access on behalf of the User. The User Institution agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the User Institution to whom the Provider Scientist grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: The Provider Scientist and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data at the Provider Institution. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Project: The project for which the User Institution has requested access on behalf of the User to the Data. A description of the Project is set out in Appendix II. Provider Scientist: for the purposes of this Agreement, he is the principal investigator of the Provider Institution in relation with the Data. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Research Participant: An individual whose data form part of these Data. Research Purposes: Shall mean non-commercial research that is seeking to advance the understanding of genetics and genomics, including the treatment of disorders, and work on statistical methods that may be applied to such research. User: The User Institution’s principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. Institution: ___________________________________________ Address: ___________________________________________ Contact Person: _____________________ Contact Phone: ______________ Contact e-mail: ________________ Terms and Conditions 1. The User Institution agrees to only use the Data for the purpose of the Project (as described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use the Data for Research Purposes which are within the limitations (if any) set out in Appendix I. 2. The User Institution agrees to preserve, at all times, the confidentiality of the Data. In particular, it undertakes not to use, or attempt to use the Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect the Data. 3. The User Institution agrees to protect the confidentiality of Research Participants in any Publications that they prepare by taking all reasonable care to limit the possibility of identification. 4. The User Institution agrees not to link or combine the Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been approved by the User Institution’s ethics body and formally granted to the User Institution or is freely available without restriction. 5. The User Institution agrees only to transfer or disclose the Data, in whole or part, or any material derived from the Data, to the Authorised Personnel. Should the User Institution wish to share the Data with an External Collaborator, the External Collaborator must complete a separate application for access to the Data. 6. The User Institution agrees that the Data Producers, and all other parties involved in the creation, funding or protection of the Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of the Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the User Institution and/or the User and/or any other authorised recipient that may arise (whether directly or indirectly) in any way whatsoever from the User Institution and/or the User and/or any other authorised recipient ’s use of these Data or from the unavailability of, or break in access to, the Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of the Data. 7. The User Institution agrees to follow the Fort Lauderdale Guidelines on sharing data from large-scale biological research projects (https://wellcome.ac.uk/sites/default/files/wtd003207_0.pdf) and the Toronto Statement (https://www.nature.com/articles/461168a.pdf) on prepublication data sharing. This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of the Data. 8. The User Institution agrees to follow the Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing the Data. 9. The User Institution agrees not to make intellectual property claims on the Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of the Data, or conclusion drawn directly from the Data. 10. The User Institution can elect to perform further research that would add intellectual and resource capital to the Data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution agrees to implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health (NIH) Best Practices for the Licensing of Genomic Inventions (Federal Register /Vol. 70, No. 68 / 2005 https://www.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (http://www.oecd.org/science/biotech/36198812.pdf , OECD 2006). 11. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the Data for archival purposes in conformity with audit or legal requirements. 12. The User Institution will notify the Provider Scientist and the Provider Institution within 30 days of any changes or departures of Authorised Personnel. Appendix III of this Agreements shall be amended in writing by the parties accordingly. 13. The User will notify the Provider Scientist and the Provider Institution prior to any significant changes to the protocol for the Project. Appendix II of this Agreements shall be amended in writing by the parties accordingly. 14. The User Institution will notify the Provider Institution as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The Provider Institution may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining the Data for archival purpose in conformity with audit or legal requirements. 16. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this Agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than the Provider Scientist. In the event that changes are required, the Provider Institution on behalf of the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 17. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this Agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorised Personnel. The User Institution will procure that the Authorised Personnel comply with the terms of this Agreement. 19. The parties will make their best efforts to amicably settle all disputes arising out of or in connection with this Agreement. In the event of any dispute, controversy or claim arising under, out of or relating to this Agreement and any subsequent amendments of this Agreement, including, without limitation, its formation, validity, binding effect, interpretation, performance, breach or termination, as well as non-contractual claims, cannot be solved amicably, they shall be submitted to mediation in accordance with the WIPO Mediation Rules. The place of mediation shall be mutually decided by the parties. The language to be used in the mediation shall be English unless otherwise agreed upon. In case that mediation efforts shall not succeed, these disputes, controversies or claims shall be submitted to a competent court. SIGNATURES IN NEXT PAGE IN WITNESS WHEREOF, the parties hereto have executed this Agreement by their duly authorized officers or representatives. Agreed by User Institution Signature: ______________________________________ Name: ______________________________________ Title: ______________________________________ Date: _____________ User Scientist I confirm that I have reviewed, am familiar with and agree to all of the above terms and conditions. I hereby undertake to fully cooperate with the User Institution in order to ensure its ability to fulfill its obligations hereunder, as set forth herein. Signature: ______________________________________ Name: ______________________________________ Title: ______________________________________ Date: _____________ Provider Institution Signature: ______________________________________ Name: ______________________________________ Title: ______________________________________ Date: _____________ Provider DAC Signature: ______________________________________ Name: ______________________________________ Title: ______________________________________ Date: _____________ Please return a signed electronic pdf copy of this Agreement to Prof. Nir Friedman (nir.friedman@mail.huji.ac.il) and to Mr. Gustavo Fuchs, Coordinator Intellectual Property and Technology, The Hebrew University of Jerusalem, the Authority for R&D (gustavof@savion.huji.ac.il). APPENDIX I – DATASET DETAILS (To be completed by the Provider Scientist) 1. Dataset reference 1.1. Dataset Identification EGA ID: ____________ Dataset Name: ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells-of-origin________________________ Other Identifiers: ¬¬¬¬¬¬¬¬______________________ 1.2. Dataset Details Access to the sequence and alignment data produced by the ChIP-seq of plasma cell-free nucleosomes experiment is controlled by the Data Access Committee (DAC). Access to data will be granted to qualified investigators for appropriate use. 2. Name and description of project that created the dataset See project description in paper _____________________________________________________________________ _____________________________________________________________________ _____________________________________________________________________ 3. Names of other data producers/collaborators Name Position and affiliation Updated Position and Affiliation Status Contact e-mail Supervisor (where applicable) Nir Friedman PI - Hebrew University of Jerusalem nir.friedman@mail.huji.ac.il Gavriel Fialkoff Hebrew University of Jerusalem Gavriel.fialkoff@mail.huji.ac.il 4. Specific limitations 4.1. User Institution agree to use the Data only for the advancement of non-commercial medical and scientific research, according to the consent given by the Data Subjects. 4.2. User Institution agree not to use the Data for the creation of products for sale or for any commercial purpose. 4.3. Other limitations by the Provider Scientist _________________________________________ 5. Minimum protection measures required File access: Data can be held in unencrypted files on an institutional compute system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should have password protected logins and screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. We anticipates that data generated from the plasma ChIP-seq project will be used by others, such as required for developing new analytical methods, in understanding epigenetics, for integrative analysis and for other uses. Authors who use data from the project must acknowledge ChIP-seq project.Users should note that the ChIP-seq project bears no responsibility for the further analysis or interpretation of these data, over and above that was published. APPENDIX II – PROJECT DETAILS (To be completed by the User-Requestor-) 1. Details of dataset requested 2. Brief abstract of the Project in which the Data will be used (500 words max) 3. All Individuals who the User Institution to be named as registered users Name of Registered User Email Job Title Supervisor* 4. All Individuals that should have an account created at the EGA Name of Registered User Email Job Title APPENDIX III – PUBLICATION POLICY DATA ACCESS AGREEMENT This DATA ACCESS AGREEMENT (this “Agreement”) made and entered into on _________201_ between the Hebrew University of Jerusalem, the Authority for R&D, Edmond J. Safra Campus, Jerusalem 91390, Israel (the "Provider Institution"), on behalf of Prof. Nir Friedman (the “Provider Scientist”); and between __________________with offices at ____________ (the “User Institution”) on behalf of Prof./Dr._______________ (the “User”), relating to the access by the User of certain data deposited by the Provider Scientist at the European Genome-phenome Archive (“EGA”) for use in a study. These terms and conditions govern access to the managed access datasets (details of which are set out in Appendix I) to which the User Institution has requested access on behalf of the User. The User Institution agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the User Institution to whom the Provider Scientist grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: The Provider Scientist and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data at the Provider Institution. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Project: The project for which the User Institution has requested access on behalf of the User to the Data. A description of the Project is set out in Appendix II. Provider Scientist: for the purposes of this Agreement, he is the principal investigator of the Provider Institution in relation with the Data. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Research Participant: An individual whose data form part of these Data. Research Purposes: Shall mean non-commercial research that is seeking to advance the understanding of genetics and genomics, including the treatment of disorders, and work on statistical methods that may be applied to such research. User: The User Institution’s principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. Institution: ___________________________________________ Address: ___________________________________________ Contact Person: _____________________ Contact Phone: ______________ Contact e-mail: ________________ Terms and Conditions 1. The User Institution agrees to only use the Data for the purpose of the Project (as described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use the Data for Research Purposes which are within the limitations (if any) set out in Appendix I. 2. The User Institution agrees to preserve, at all times, the confidentiality of the Data. In particular, it undertakes not to use, or attempt to use the Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect the Data. 3. The User Institution agrees to protect the confidentiality of Research Participants in any Publications that they prepare by taking all reasonable care to limit the possibility of identification. 4. The User Institution agrees not to link or combine the Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been approved by the User Institution’s ethics body and formally granted to the User Institution or is freely available without restriction. 5. The User Institution agrees only to transfer or disclose the Data, in whole or part, or any material derived from the Data, to the Authorised Personnel. Should the User Institution wish to share the Data with an External Collaborator, the External Collaborator must complete a separate application for access to the Data. 6. The User Institution agrees that the Data Producers, and all other parties involved in the creation, funding or protection of the Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of the Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the User Institution and/or the User and/or any other authorised recipient that may arise (whether directly or indirectly) in any way whatsoever from the User Institution and/or the User and/or any other authorised recipient ’s use of these Data or from the unavailability of, or break in access to, the Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of the Data. 7. The User Institution agrees to follow the Fort Lauderdale Guidelines on sharing data from large-scale biological research projects (https://wellcome.ac.uk/sites/default/files/wtd003207_0.pdf) and the Toronto Statement (https://www.nature.com/articles/461168a.pdf) on prepublication data sharing. This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of the Data. 8. The User Institution agrees to follow the Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing the Data. 9. The User Institution agrees not to make intellectual property claims on the Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of the Data, or conclusion drawn directly from the Data. 10. The User Institution can elect to perform further research that would add intellectual and resource capital to the Data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution agrees to implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health (NIH) Best Practices for the Licensing of Genomic Inventions (Federal Register /Vol. 70, No. 68 / 2005 https://www.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (http://www.oecd.org/science/biotech/36198812.pdf , OECD 2006). 11. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the Data for archival purposes in conformity with audit or legal requirements. 12. The User Institution will notify the Provider Scientist and the Provider Institution within 30 days of any changes or departures of Authorised Personnel. Appendix III of this Agreements shall be amended in writing by the parties accordingly. 13. The User will notify the Provider Scientist and the Provider Institution prior to any significant changes to the protocol for the Project. Appendix II of this Agreements shall be amended in writing by the parties accordingly. 14. The User Institution will notify the Provider Institution as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The Provider Institution may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining the Data for archival purpose in conformity with audit or legal requirements. 16. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this Agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than the Provider Scientist. In the event that changes are required, the Provider Institution on behalf of the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 17. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this Agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorised Personnel. The User Institution will procure that the Authorised Personnel comply with the terms of this Agreement. 19. The parties will make their best efforts to amicably settle all disputes arising out of or in connection with this Agreement. In the event of any dispute, controversy or claim arising under, out of or relating to this Agreement and any subsequent amendments of this Agreement, including, without limitation, its formation, validity, binding effect, interpretation, performance, breach or termination, as well as non-contractual claims, cannot be solved amicably, they shall be submitted to mediation in accordance with the WIPO Mediation Rules. The place of mediation shall be mutually decided by the parties. The language to be used in the mediation shall be English unless otherwise agreed upon. In case that mediation efforts shall not succeed, these disputes, controversies or claims shall be submitted to a competent court. SIGNATURES IN NEXT PAGE IN WITNESS WHEREOF, the parties hereto have executed this Agreement by their duly authorized officers or representatives. Agreed by User Institution Signature: ______________________________________ Name: ______________________________________ Title: ______________________________________ Date: _____________ User Scientist I confirm that I have reviewed, am familiar with and agree to all of the above terms and conditions. I hereby undertake to fully cooperate with the User Institution in order to ensure its ability to fulfill its obligations hereunder, as set forth herein. Signature: ______________________________________ Name: ______________________________________ Title: ______________________________________ Date: _____________ Provider Institution Signature: ______________________________________ Name: ______________________________________ Title: ______________________________________ Date: _____________ Provider DAC Signature: ______________________________________ Name: ______________________________________ Title: ______________________________________ Date: _____________ Please return a signed electronic pdf copy of this Agreement to Prof. Nir Friedman (nir.friedman@mail.huji.ac.il) and to Mr. Gustavo Fuchs, Coordinator Intellectual Property and Technology, The Hebrew University of Jerusalem, the Authority for R&D (gustavof@savion.huji.ac.il). APPENDIX I – DATASET DETAILS (To be completed by the Provider Scientist) 1. Dataset reference 1.1. Dataset Identification EGA ID: ____________ Dataset Name: ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells-of-origin________________________ Other Identifiers: ¬¬¬¬¬¬¬¬______________________ 1.2. Dataset Details Access to the sequence and alignment data produced by the ChIP-seq of plasma cell-free nucleosomes experiment is controlled by the Data Access Committee (DAC). Access to data will be granted to qualified investigators for appropriate use. 2. Name and description of project that created the dataset See project description in paper _____________________________________________________________________ _____________________________________________________________________ _____________________________________________________________________ 3. Names of other data producers/collaborators Name Position and affiliation Updated Position and Affiliation Status Contact e-mail Supervisor (where applicable) Nir Friedman PI - Hebrew University of Jerusalem nir.friedman@mail.huji.ac.il Gavriel Fialkoff Hebrew University of Jerusalem Gavriel.fialkoff@mail.huji.ac.il 4. Specific limitations 4.1. User Institution agree to use the Data only for the advancement of non-commercial medical and scientific research, according to the consent given by the Data Subjects. 4.2. User Institution agree not to use the Data for the creation of products for sale or for any commercial purpose. 4.3. Other limitations by the Provider Scientist _________________________________________ 5. Minimum protection measures required File access: Data can be held in unencrypted files on an institutional compute system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should have password protected logins and screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. We anticipates that data generated from the plasma ChIP-seq project will be used by others, such as required for developing new analytical methods, in understanding epigenetics, for integrative analysis and for other uses. Authors who use data from the project must acknowledge ChIP-seq project.Users should note that the ChIP-seq project bears no responsibility for the further analysis or interpretation of these data, over and above that was published. APPENDIX II – PROJECT DETAILS (To be completed by the User-Requestor-) 1. Details of dataset requested 2. Brief abstract of the Project in which the Data will be used (500 words max) 3. All Individuals who the User Institution to be named as registered users Name of Registered User Email Job Title Supervisor* 4. All Individuals that should have an account created at the EGA Name of Registered User Email Job Title APPENDIX III – PUBLICATION POLICY The Provider Scientist intend to publish the results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. The Provider Scientist anticipate that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication should not occur until _______ months after these data were first made available on the relevant hosting database, unless The Provider Scientist and the Provider Institution have provided written consent to earlier submission. In any publications of the User based on the Data (as defined in this Agreement), the User shall describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (e.g., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with the Provider Scientist. The Provider Scientist intend to publish the results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. The Provider Scientist anticipate that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication should not occur until _______ months after these data were first made available on the relevant hosting database, unless The Provider Scientist and the Provider Institution have provided written consent to earlier submission. In any publications of the User based on the Data (as defined in this Agreement), the User shall describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (e.g., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with the Provider Scientist.