Terms and Conditions, 11.07.2023

Welcome to the SinCMat web application, a software provided by the Luxembourg Centre for Systems Biomedicine, an interdisciplinary centre of the University of Luxembourg.

The below Terms and Conditions apply to all agreements by and between the University of Luxembourg and a User (as defined below) with respect to the use of the SinCMat web application and to all legal acts in connection therewith.

Please read these Terms and Conditions carefully before using the SinCMat web application. By using the SinCMat web application, you signify your agreement to these Terms and Conditions. Upon acceptance – by using SinCMat - of these Terms and Conditions, such Terms and Conditions become the Agreement (as defined below) between the University of Luxembourg and the User. If you do not agree to these Terms and Conditions, you may not use the SinCMat web application.

The Provider (as defined below) may modify these Terms and Conditions at any time by updating this posting. The User is bound by any such modification and will be informed of each update before its use of the SinCMat web application. The applicable Terms and Conditions are the ones on the website at the time of the use.

  1. Definition:

    As used in these Terms and Conditions, the following terms, when used in capital letters, shall have the following meanings:

    Agreement: The agreement by and between the Provider and the User, in which the Provider authorises the User to use the SinCMat web application. The modalities of such Agreement are defined by the present Terms and Conditions.

    Applicable Data Protection Laws: Any applicable national law of Luxembourg related to Data Protection and enforcing the General Data Protection Regulation (EU) 2016/679 or any superseding text.

    User: The natural person or legal entity that enters into an Agreement with the Provider.

    Provider: The University of Luxembourg, an institution of higher education and research, having its registered office at 2 avenue de l’Université, L-4365 Esch-sur-Alzette, Luxembourg, acting for its Luxembourg Centre for System Biomedicine, an interdisciplinary centre.

    Parties: The User and the Service Provider.

    License: the authorisation to use the SinCMat web application granted to the User by the Provider in compliance with the Agreement.

    SinCMat web application: The SinCMat web application is a software that enables users to identify the transcription factors (TFs) that are involved in the maturation of a specific cell type. It includes 3 sections: the webtool, which enables users to apply SinCMat algorithm to their specific target cell, the database which allows the users to browse all maturation TF evidences collected from the literature, and finally, an atlas section that provides maturation TFs for a series of mouse and human celltypes

    PAWS SinCMat: A website hosting the SinCMat web application.

    PAWS: “Pipeline As a Web Service” is the software framework supporting the PAWS Platform.

    Results: Results of the analysis carried by the SinCMat web application.

    the following words have the same meaning as in the European Regulation 2016/679 named General Data Protection Regulation (“GDPR”): “Controller”, “Processor”, “Data Subject”, “Personal Data”, “Data Protection Officer”, “Pseudonymisation”, “Consent” and “Processing”.

  2. PAWS Platform:

    The User can place an enquiry on the PAWS Platform. By doing so, the User understands and agrees that the Provider might collect and process its Personal Data (as defined by the European Regulation 2016/679 mentioned below) for the purposes of allocating account details to the User and granting it the License.

    The User agrees to provide, maintain and update true, accurate, current and complete information about itself. The User agrees not to impersonate any person or entity or misrepresent its identity or affiliation with any person or entity, including using another person's username, password or any other account information.

    The content available on the PAWS Platform, such as text, graphics, images, audio, video and other material, as well as the domain names, tagline, organisation and user look-and-feel (collectively, the "Content"), is protected by copyright, trademark and other intellectual property rights in Luxembourg and foreign countries, and is owned or controlled by the Provider or by third parties that have licensed their Content to the Provider. Unauthorized use of the Content may violate copyright, trademark, and other intellectual property rights.

  3. Using the Software:

    The User can use the Software by:

      Webtool offers an intuitive interface to predict maturation TF using your own single-cell RNA-seq dataset. To use:
    1. Navigate to the Webtool panel.
      • Choose the species (Mouse or Human) of your single-cell RNA seq data.
      • Upload the scRNA-seq data of your target cell type in a tab-delimited text file (.txt) format. Ensure the gene expression matrix has gene symbols as row names and cell identifiers/barcodes as column names. An example input file is available in the Webtool panel for reference.
      • Optionally, you can submit your email address for notifications when the output files are ready.
      Output Files:
      • Final_predictions_User.tsv: This file lists ITF/STF pairs predicted by SinCMat, along with their related maturation score and the number of functional co-target genes.
      • Cobinding_result_User.csv: This file presents results for all possible ITF/STF combinations, detailing the Jaccard index score, number of common target genes, sum of Pearson correlation scores, and maturation score.
      By using the SinCMat Webtool, the User can download the Results, share the Results - on a restricted access basis - and benefit from the Results from more than one Set of Input Files at a time. The Results it contains, will be deleted from the SinCMat by the Provider should no activity be reported 6 (six) months after the delivery of the last Results to the User.
  4. User Obligations:

    The User agrees and acknowledges that any failure to provide, either in quality and/or in quantity, the Set(s) of Input Files or any other information or material in accordance with the Agreement will delay the supply of the Results and that the Provider shall not be liable to the User in respect of any such failure of the User.

    The User represents and warrants that: (i) it owns or has the right to provide the Set(s) of Input Files to the Provider for use in connection with the Software, and such delivery and use will not violate any obligation that the User owes to any third party; (ii) it has secured all necessary approvals, licenses and permits to upload the Set(s) of Input Files on the SinCMat web application ; (iii) the processing of the Set(s) of Input Files by the Software for the performance of the analysis by the Software will not infringe any intellectual property or other proprietary rights of any third party, nor violate any legal or ethical requirements.

    In the event of any breach of any of the foregoing representations and warranties, the User shall indemnify and hold harmless the Provider, and its respective directors, officers, employees, representatives, licensors and agents from and against any loss, costs, damages, liabilities or claims of any kind relating to such breach. The User is responsible for the clearance of the rights on the Set(s) of Input Files

  5. Delivery of Results:

    When available, the Software will send an email to inform the User that the Results can be viewed.

    If the User has uploaded the Set of Input Files with an email, it will receive an email with a link and an access token, to allow the User to access to the Results.

    The Licence shall be deemed to be completed upon delivery of the Results. The Provider shall have no obligation to grant any further Licences and shall not be required to deliver any copy of the Results.

    The Provider will delete the Set(s) of Input Files upon delivery of the Results.

  6. Payment:

    The Licence is provided on a free-of-charge basis.

  7. Object of the License and Intellectual Property:

    The User allows the Provider to process the Set(s) of Input Files through its SinCMat web application, for the purpose of analysing the Set(s) of Input Files.

    The User becomes the owner of the Results upon delivery of such Results.

    The Provider's may, at its discretion and when appropriate, terminate the account of any User who may infringe, or has infringed the copyrights of third parties.

  8. Use of the Results:

    The Software aims to provide a tool to support computational biology research. It is NOT approved for clinical use. The User shall use the Results at its own discretion and its own risk.

    The Provider makes no representations or warranties about the accuracy, reliability or completeness to be obtained from using the Results.

  9. Data Protection:
    9.1 Placing an order:

    To the extent that the User provides Personal Data to place an enquiry with or without creating an account, the Provider will be considered Controller regarding such Personal Data.

    In such case, the Provider will collect and store the Personal Data of the User for the sole purpose of providing the User with an account on the PAWS Platform and/or delivering the Results to the User. The Personal Data will be stored securely and will be deleted by the Provider according to Section 3 of the present Terms and Conditions.

    The processing of your personal data is necessary for the performance of the Terms and conditions in accordance with article 6(1) ( b) of the GDPR.

    According to the GDPR, the Client has the right to access to its Personal Data, and to ask the Service Provider for modification or deletion of such Personal Data. In case of any queries regarding his/her personal data the Client can contact the Data Protection Officer of the University on dpo@uni.lu during working hours or following the procedure available on https://wwwen.uni.lu/university/data_protection/your_rights.

    If you consider the Processing of your Personal Data infringes your rights, you can lodge a complaint to the CNPD. Information is provided on http://www.cnpd.lu.

    By placing an enquiry, the User expressly acknowledges the collection and processing of its Personal Data.

    9.2 Performance of the Service:

    For the purpose of the Licence, the User is a Data Controller and the Provider is a Data Processor.

    By providing the Set of Input Files, data containing Personal Data might be transferred from the User to the Provider. By requesting the Licence, the User instructs the Provider to Process such Personal Data.

    Each Party shall be responsible for complying with all Data Protection requirements. The User ensures to provide only Personal Data obtained and processed in accordance with the Applicable Data Protection Laws, which have undergone Pseudonymization. The User is responsible for ensuring that the Consent of the Data Subject has been documented and given and that it covers the execution of the analysis by the Software. The User is responsible for enforcing Data Subject’s statutory rights. If any of these requirements is not met, the Agreement shall be terminated and the Provider shall not be held responsible for any loss, harm or damage generated in connection with such termination. The Provider is not liable for any misuse of the Personal Data by the User.

    The Provider shall only Process Data, which have undergone Pseudonymization and ensures that such Personal Data shall not be stored nor retained during a period of time superior to one (1) or six (6) months after the date of the delivery of the last Results as stated under Section 3. The Provider shall ensure that the Processing of the Personal Data is made in compliance with Applicable Data Protection Laws requirements. The Provider shall not share any Personal Data and it will not undertake any action in order to identify any Data Subject.

    Furthermore, the Provider as a Processor of the Personal Data warrants and undertakes to:

      Process the Personal Data only upon written and documented instructions, including in electronic form, from the Controller;

      Authorize only employees to Process the Personal Data under the condition that their obligations related to confidentiality are adequate to comply with the GDPR;

      Ensure the confidentiality, the integrity and availability of the Personal Data;

      Assist the Controller in treating Data Subject’s queries, within the limits of the nature to the framework of the Processing;

      Assisting the Controller in ensuring its duties with regards to the statutory rights of the Data Subject;

      Delete all Personal Data contained in the Set(s) of Input Files after delivery of the Results;

      If required by the Controller, demonstrate the compliance with the above-mentioned measures and allow for audits conducted by the Controller or an auditor mandated by the Controller strictly limited to the matter hereto. The audit shall be undertaken upon at least two weeks of prior notice. The audit will occur during the opening hours of the Processor and will be limited to the Controller’s Personal Data. In no circumstances, the Controller may audit the Personal Data of other Users or access to Personal Data not relevant to the processing of the Licences it has asked. The Processor may ask for a fee regarding to the organisation of the audit.

      Inform the Controller if an instruction from it seems to infringe the data protection laws.

    The Controller represents and warrants that information about the presence of Personal Data could be provided with the Set of Input Files and that the enquiry is either not a further (or “secondary”) processing, or that, if the case, the enquiry complies with articles 5.1, 6.4 and 89 of the GDPR.

    The Parties shall not transfer Personal Data to a country outside of the European Economic Area without complying with applicable data protection laws.

    The Parties agree to cooperate fully with each other for responding to requests from supervisory authorities under Article 31 GDPR.

    The Parties shall not release any Data to any person or entity other than those involved in the performance of the Licence, and on a strict need-to-know basis.

  10. Liability:

    The Provider provides the License for free and as is. It shall not be liable for any consequence of the use of the License by the User.

    In particular, Provider shall not be liable for (1) any inaccuracy, error in or failure of the SinCMat web application, (2) or any loss or damage (including without limitation any consequential, indirect, incidental, special or exemplary damages) arising from such inaccuracy, error in or failure of the SinCMat web application, (3) or any loss or damage (including without limitation any consequential, indirect, incidental, special or exemplary damages) arising from any download or use made of the Results. If any of the above provisions are void under applicable law, the Provider's liability shall be limited to the full extent permitted by law.

  11. Indemnity:

    The User agrees to defend, indemnify, and hold harmless the Provider, its officers, directors, employees and agents, from and against any claims, actions or demands, including without limitation reasonable legal and accounting fees, alleging or resulting from the User’s breach of these Terms of Use. This indemnification provision does not apply to wilful misconduct or gross negligence on the part of the Provider.

  12. Termination:

    The Provider is entitled, without further notice of default and without written intervention, to terminate with immediate effect the Agreement, if the User fails to fulfil any of its obligations under these Terms and Licences.

  13. Applicable Laws and Jurisdiction:

    Any dispute arising from the interpretation and/or implementation of these Terms and Conditions, which cannot be settled amicably, shall be brought before a competent court in the city of Luxembourg.