{"id":2130,"date":"2025-10-22T13:23:31","date_gmt":"2025-10-22T11:23:31","guid":{"rendered":"https:\/\/wp.unil.ch\/dsbu\/?p=2130"},"modified":"2025-10-29T13:22:19","modified_gmt":"2025-10-29T12:22:19","slug":"from-bench-to-fair-data-practical-approaches-to-research-data-management-in-life-science-and-clinical-research","status":"publish","type":"post","link":"https:\/\/wp.unil.ch\/dsbu\/from-bench-to-fair-data-practical-approaches-to-research-data-management-in-life-science-and-clinical-research\/","title":{"rendered":"Workshop: &#8220;From Bench to FAIR Data: Practical Approaches to Research Data Management in Life Science and Clinical Research&#8221;"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\"><em>FBM PhD course open to Postdoctoral researchers and data managers<\/em><\/h2>\n\n\n\n<p>Co-organized by the\u00a0<strong>DSBU, University Center for\u00a0Primary Care and Public <\/strong>\u00a0and the\u00a0<strong>FBM Doctoral School<\/strong><\/p>\n\n\n\n<p><strong>Thursday 27 November &amp; Thursday 4 December 2025<\/strong><br><strong>&nbsp;\u2013 In-person sessions<\/strong><\/p>\n\n\n\n<p><strong>From 9:15 to 17:30<\/strong><\/p>\n\n\n\n<p><strong>Room 2144, G\u00e9opolis Building, Quartier Mouline \u2013 University of Lausanne<\/strong> (Metro M1 line, Mouline station)<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Course Structure<\/strong><\/h2>\n\n\n\n<p>The course is organized into three sessions: <strong>two full-day in-person workshops (Days 1 and 3)<\/strong> and <strong>one self-paced practical session in between<\/strong>.<\/p>\n\n\n\n<p>The in-person sessions are <strong>divided into four modules<\/strong> that combine theory with practical exercises using real data examples and institutional tools.<\/p>\n\n\n\n<p>During the <strong>first three modules<\/strong>, <strong>all participants<\/strong> will work together to cover the organization and management of research data, the creation of clear documentation and standardized metadata using institutional tools, and the principles of FAIR data sharing and long-term preservation.<\/p>\n\n\n\n<p><strong>The fourth module <\/strong>will take place in <strong>two parallel sessions<\/strong>:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>The first group<\/strong> will include participants working with <strong>sensitive or clinical data<\/strong>, focusing on de-identification, restricted data sharing, and confidentiality management.<\/li>\n\n\n\n<li><strong>The second group<\/strong> will target participants <strong>working in life science research<\/strong>, deepening their understanding of FAIR data sharing in specialized repositories (e.g., ENA, BIA) and the use of metadata standards specific to life science data.<\/li>\n<\/ul>\n\n\n\n<p><strong>Between the two in-person workshop days<\/strong>, participants will complete <strong>a self-paced practical exercise at home<\/strong>, applying the concepts learned to their own datasets. This work will then be discussed and consolidated during the final in-person sessions<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Overview<\/strong><\/h2>\n\n\n\n<p>The exponential growth of research data in life sciences and clinical research has made it crucial to implement robust <strong>Research Data Management (RDM)<\/strong> strategies based on <strong>Open Research Data<\/strong> practices.<\/p>\n\n\n\n<p>Applying the <strong>FAIR principles<\/strong> (<em>Findable, Accessible, Interoperable and Reusable<\/em>) brings major benefits: improving data visibility, reproducibility, reusability, and credibility, while enabling new scientific collaborations and research questions.<\/p>\n\n\n\n<p>This <strong>two-day theoretical and hands-on workshop<\/strong>, co-organized by the <strong>Data Stewardship BioMed Unit (DSBU)<\/strong> and the <strong>FBM Doctoral School<\/strong>, offers a practical and comprehensive introduction to RDM and the FAIR principles in the context of life sciences and clinical research.<\/p>\n\n\n\n<p>Through a mix of lectures and guided exercises, participants will learn to manage their data according to FAIR and reproducible research standards and to use institutional and open-source tools to support these practices.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Target Audience<\/strong><\/h2>\n\n\n\n<p>This workshop is <strong>reserved for members of the Faculty of Biology and Medicine (FBM)<\/strong> at the <strong>University of Lausanne (UNIL)<\/strong> and the <strong>University Hospital of Lausanne (CHUV)<\/strong>.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>PhD students<\/strong> in life sciences or clinical research handling digital research data<\/li>\n\n\n\n<li><strong>Postdoctoral researchers and data managers<\/strong>, including those fulfilling data management roles in research laboratories<\/li>\n\n\n\n<li><strong>For PIs<\/strong>, <strong>shorter and tailored training sessions are organized separately<\/strong> for their research groups, focusing on the specific data types and research themes of individual groups. PIs interested in customized workshops related to their own research are encouraged to <a href=\"https:\/\/wp.unil.ch\/dsbu\/contact\/\" target=\"_blank\" rel=\"noreferrer noopener\">contact us<\/a>.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Learning Outcomes<\/strong><\/h2>\n\n\n\n<p>By the end of the course, participants will have acquired both theoretical and practical skills to implement <strong>FAIR and reproducible Research Data Management (RDM)<\/strong> practices throughout the research lifecycle.<\/p>\n\n\n\n<p>Participants will learn to:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Organize research data efficiently and select appropriate file formats for FAIR sharing and long-term preservation<\/li>\n\n\n\n<li>Develop and update Data Management Plans (DMPs) using the <strong>Data Stewardship Wizard (DSW)<\/strong><\/li>\n\n\n\n<li>Document datasets with <strong>README files<\/strong> and metadata using <strong>DataSquid<sup>@DSBU<\/sup><\/strong> for semi-automated data documentation<\/li>\n\n\n\n<li>Integrate and harmonize metadata across systems and deposit datasets in <strong>FAIR-compliant repositories<\/strong> (e.g., <strong>FBM Zenodo Community<\/strong>, <strong>ENA<\/strong> for sequencing data, <strong>BIA<\/strong> for imaging data, or the <strong>Horus Dataset Catalog CHUV<\/strong> for sensitive clinical data)<\/li>\n\n\n\n<li>Assess and mitigate risks for sensitive data, applying appropriate security and de-identification measures, and ensuring compliance with ethical and legal standards<\/li>\n\n\n\n<li>Understand the principles of <strong>long-term data preservation<\/strong> via<strong> tape-based archiving solutions<\/strong><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Course Structure<\/strong><\/h2>\n\n\n\n<p>Each module combines a <strong>theoretical introduction<\/strong> with <strong>hands-on exercises<\/strong> using real data examples and institutional tools.<\/p>\n\n\n\n<p>The course is structured over three main sessions with two <strong>in person <\/strong>(Days 1 and 3) and one <strong>self-paced practical session<\/strong> in between.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><strong>Day 1 \u2013 Thursday, 27 November 2025  (Full day <strong>from 9:15 to 17:30<\/strong>, in person)<\/strong><\/h3>\n\n\n\n<h4 class=\"wp-block-heading\"><strong>Module I: Data Types &amp; Organization<\/strong><\/h4>\n\n\n\n<p>Participants will be introduced to best practices in data and file management across the research lifecycle.<\/p>\n\n\n\n<p>Topics include:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Data entry validation, folder structure, file naming and file formats<\/li>\n\n\n\n<li>Selecting sustainable file formats for sharing and preservation<\/li>\n\n\n\n<li>Creating personalized DMP using <a href=\"https:\/\/wp.unil.ch\/dsbu\/tools\/\">Data Stewardship Wizard (DSW) tool<\/a><\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\"><strong>Module II: Data Documentation<\/strong><\/h4>\n\n\n\n<p>During this module, participants will enhance their data documentation skills through metadata and README files, using tools to facilitate efficient data organization, storage, retrieval, and sharing.<\/p>\n\n\n\n<p>Participants will learn how to:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>apply&nbsp;metadata standards <\/li>\n\n\n\n<li>create structured <strong>README files<\/strong>&nbsp;using <a href=\"https:\/\/wp.unil.ch\/dsbu\/tools_readme\/\" target=\"_blank\" rel=\"noreferrer noopener\">DataSquid<\/a><sup>@DSBU<\/sup>&nbsp;<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\"><strong>Day 2 \u2013 Independent work (self-paced practicals)<\/strong><\/h3>\n\n\n\n<p>Between the two in-person sessions, participants will dedicate half a day to practicing with <a href=\"https:\/\/wp.unil.ch\/dsbu\/tools\/\">Data Stewardship Wizard (DSW) tool<\/a> and <a href=\"https:\/\/wp.unil.ch\/dsbu\/tools_readme\/\" target=\"_blank\" rel=\"noreferrer noopener\">DataSquid<\/a><sup>@DSBU<\/sup>on their own research data.<\/p>\n\n\n\n<p>This independent work, carried out on the participants&#8217; own time, allows them to apply concepts introduced during the first day.<\/p>\n\n\n\n<p>Questions and issues raised during this time will be addressed collectively in the final session through demonstrations and targeted feedback.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><strong>Day 3 \u2013 Thursday, 4 December 2025 (Full day <strong><strong>from 9:15 to 17:30<\/strong><\/strong>, in person)<\/strong><\/h3>\n\n\n\n<h4 class=\"wp-block-heading\"><strong>Module III: Metadata Integration and FAIR Repositories<\/strong><\/h4>\n\n\n\n<p>This module focuses on the <strong>practical application of FAIR data-sharing workflows<\/strong>, from metadata integration and documentation to dataset deposition and publication. <\/p>\n\n\n\n<p>Participants will be introduced to <strong>long-term data preservation and archiving<\/strong>.<\/p>\n\n\n\n<p>Through <strong>demonstrations and hands-on exercises<\/strong>, participants will practice how to:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Identify the right repository for their research data and prepare and structure metadata for deposition using <a href=\"https:\/\/FAIRShare Explorer \u00a9DSBU https:\/\/dsbu.unil.ch\/datasquid-fbm\/repositories\">FAIRShare Explorer<\/a><\/li>\n\n\n\n<li>Upload, describe, and publish datasets on specialized repositories such as <a href=\"https:\/\/zenodo.org\/communities\/fbm_chuv\/records?q=&amp;l=list&amp;p=1&amp;s=10&amp;sort=newest\">FBM Zenodo Community<\/a>, <a href=\"https:\/\/www.ebi.ac.uk\/ena\/browser\/submit\">ENA<\/a> and <a href=\"https:\/\/www.ebi.ac.uk\/bioimage-archive\/submit\/\">BioImage Archive<\/a>. <\/li>\n\n\n\n<li>Reuse, copyright, and license data.<\/li>\n\n\n\n<li>Ensure secure<strong>&nbsp;<\/strong><a href=\"https:\/\/wp.unil.ch\/dsbu\/consulting-research-data-storage\/#Long-Term-Storage\">long-term preservation<\/a>&nbsp;through tape-based archiving<strong>.<\/strong><\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\"><strong>Module IV<\/strong><\/h4>\n\n\n\n<p><strong>Two parallel sessions<\/strong> will take place during this module. The f<strong>irst targets participants handling sensitive data<\/strong>, while the s<strong>econd will be for researchers in Life Sciences<\/strong> to practice depositing data on specialized repositories.<\/p>\n\n\n\n<h4 class=\"wp-block-heading\"><strong>Module IV<\/strong> &#8211; <strong><strong>Orientation Data Protection for Researchers handling <strong><strong>Personal and Sensitive Data<\/strong> <\/strong><\/strong><\/strong><\/h4>\n\n\n\n<p>The Data protection module will provide <strong>practical guidance on managing and sharing sensitive data<\/strong> in compliance with ethical, legal, and institutional frameworks.<\/p>\n\n\n\n<p>Participants will learn to:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Assess data sensitivity and apply <strong>risk mitigation strategies<\/strong><\/li>\n\n\n\n<li>Use <strong>de-identification <\/strong>techniques to enable secure data reuse<\/li>\n\n\n\n<li>Metadata sharing for sensitive datasets using the <a href=\"https:\/\/wp.unil.ch\/dsbu\/1725-2\/\">HORUS Dataset Catalog (CHUV)<\/a> developed by the <strong>Data Science Group \u2013 DSI<\/strong>.<\/li>\n<\/ul>\n\n\n\n<h4 class=\"wp-block-heading\"><strong>Module IV<\/strong> &#8211; <strong><strong>Orientation Life Science for Researchers at UNIL<\/strong><\/strong><\/h4>\n\n\n\n<p>The Life science module will provide deepen practices of <strong>FAIR data sharing<\/strong> within <strong>specialized repositories<\/strong> (e.g., <strong>ENA<\/strong>, <strong>BioImage Archive<\/strong>).<\/p>\n\n\n\n<p>Participants will gain hands-on experience in:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Depositing sequencing and imaging data<\/strong> in repositories such as <a href=\"https:\/\/www.ebi.ac.uk\/ena\/browser\/submit\">ENA<\/a> and <a href=\"https:\/\/www.ebi.ac.uk\/bioimage-archive\/submit\/\">BioImage Archive<\/a>, using either participants\u2019 <strong>own data<\/strong> or a <strong>provided dataset<\/strong><\/li>\n\n\n\n<li>Exploring DataSquid and its integration within UNIL\u2019s DCSR infrastructures, with a <strong>deeper practical focus on data documentation<\/strong> for <strong>short-term and long-term storage (LTS)<\/strong>, to <strong>preserve, secure, and safeguard their research data<\/strong><br><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Evaluation and Credits for PhD Students<\/strong><\/h2>\n\n\n\n<p><strong>1 ECTS credit<\/strong> awarded upon:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Active participation during the workshop<\/li>\n\n\n\n<li>Short presentation of practical outcomes<\/li>\n\n\n\n<li>Completion of the independent work (no final written exam)<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Teachers<\/strong><\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>C\u00e9cile Lebrand, PhD<\/strong>, Head of the DSBU, FBM UNIL\u2013CHUV<\/li>\n\n\n\n<li><strong>Vassilios Ioannidis, PhD<\/strong>, Lead Computational Biologist \u2013 FAIR Data Specialist, DSBU, FBM UNIL\u2013CHUV<\/li>\n\n\n\n<li><strong>St\u00e9phanie Battini, PhD<\/strong>, Biomedical Data Scientist, DSBU, FBM UNIL\u2013CHUV<\/li>\n\n\n\n<li><strong>Julien D\u00e9n\u00e9r\u00e9az, PhD<\/strong>, Biomedical Data Scientist, DSBU, FBM UNIL\u2013CHUV<\/li>\n\n\n\n<li><strong>Clara Heiman, PhD<\/strong>, Data Steward, DSBU, FBM UNIL\u2013CHUV<\/li>\n\n\n\n<li><strong>C\u00e9line Racine, <\/strong>Head of the Documentation and Data Unit &amp; Research Data Management Specialist, Research Support Division, University Center for\u00a0Primary Care and Public <\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Requirements<\/strong><\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Participants must bring their own <strong>laptop<\/strong>.<\/li>\n\n\n\n<li>They should also come with a <strong>dataset from their own research<\/strong> that needs to be documented, as well as a <strong>clear understanding of the instruments, software, and data acquisition workflows<\/strong> used in their laboratory.<\/li>\n\n\n\n<li>This will allow participants to apply the concepts and tools presented during the workshop directly to their own research context.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>References &amp; Resources<\/strong><\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Wilkinson, M. et al. <em>The FAIR Guiding Principles for scientific data management and stewardship.<\/em> <em>Sci Data<\/em> 3, 160018 (2016). <a href=\"https:\/\/doi.org\/10.1038\/sdata.2016.18\">DOI: 10.1038\/sdata.2016.18<\/a><\/li>\n\n\n\n<li>Baker, M. <em>1,500 scientists lift the lid on reproducibility.<\/em> <em>Nature<\/em> 533, 452\u2013454 (2016). <a href=\"https:\/\/doi.org\/10.1038\/533452a\">DOI: 10.1038\/533452a<\/a><\/li>\n\n\n\n<li>Begley, C.G. &amp; Ioannidis, J.P.A. <em>Reproducibility in science: improving the standard for basic and preclinical research.<\/em> <em>Circ. Res.<\/em> 116(1):116\u2013126 (2015). <a href=\"https:\/\/doi.org\/10.1161\/CIRCRESAHA.114.303819\">DOI: 10.1161\/CIRCRESAHA.114.303819<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/wp.unil.ch\/dsbu\/sharing\/\" data-type=\"link\" data-id=\"https:\/\/wp.unil.ch\/dsbu\/sharing\/\" target=\"_blank\" rel=\"noreferrer noopener\">DSBU Website: Link<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/wp.unil.ch\/dsbu\/sharing\/\" target=\"_blank\" rel=\"noreferrer noopener\">FAIR Data Sharing &amp;&nbsp;Open Research Data Support for FBM UNIL-CHUV Researchers<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/rdmkit.elixir-europe.org\/index.html\" target=\"_blank\" rel=\"noreferrer noopener\">RDMkit \u2013 The ELIXIR Research Data Management Kit<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/wp.unil.ch\/dsbu\/tools_readme\/\" target=\"_blank\" rel=\"noreferrer noopener\">DataSquid\u00a9 \u2013 FBM Tool for Metadata &amp; README Files<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/zenodo.org\/communities\/fbm_chuv\/?page=1&amp;size=20\" target=\"_blank\" rel=\"noreferrer noopener\">FBM Zenodo Community<\/a><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Registration<\/strong><\/h2>\n\n\n\n<p>Registration via the <strong><a href=\"https:\/\/wp.unil.ch\/dsbu\/contact\/\" target=\"_blank\" rel=\"noreferrer noopener\">DSBU contact form<\/a><\/strong> <\/p>\n\n\n\n<p>Participation is <strong>free of charge<\/strong>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>FBM PhD course open to Postdoctoral researchers and data managers Co-organized by the\u00a0DSBU, University Center for\u00a0Primary Care and Public \u00a0and the\u00a0FBM Doctoral School Thursday 27 November &amp; Thursday&hellip;<\/p>\n","protected":false},"author":1002839,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"template-full-width.php","format":"standard","meta":{"_seopress_robots_primary_cat":"","_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","footnotes":""},"categories":[4],"tags":[],"class_list":{"0":"post-2130","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-courses"},"_links":{"self":[{"href":"https:\/\/wp.unil.ch\/dsbu\/wp-json\/wp\/v2\/posts\/2130","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wp.unil.ch\/dsbu\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/wp.unil.ch\/dsbu\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/dsbu\/wp-json\/wp\/v2\/users\/1002839"}],"replies":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/dsbu\/wp-json\/wp\/v2\/comments?post=2130"}],"version-history":[{"count":4,"href":"https:\/\/wp.unil.ch\/dsbu\/wp-json\/wp\/v2\/posts\/2130\/revisions"}],"predecessor-version":[{"id":2166,"href":"https:\/\/wp.unil.ch\/dsbu\/wp-json\/wp\/v2\/posts\/2130\/revisions\/2166"}],"wp:attachment":[{"href":"https:\/\/wp.unil.ch\/dsbu\/wp-json\/wp\/v2\/media?parent=2130"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/wp.unil.ch\/dsbu\/wp-json\/wp\/v2\/categories?post=2130"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/wp.unil.ch\/dsbu\/wp-json\/wp\/v2\/tags?post=2130"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}