[Community Meeting 2024] Supporting and financing RDM projects within GerBI

Overview of GerBI RDM projects: why & how? Supporting and financing RDM projects within GerBI Stefanie Weidtkamp-Peters, Josh Moore, Christian Schmidt, Roland Nitschke, Susanne Kunis, Thomas Zobel 04.03.2024 08.03.2024 GerBI Community Meeting 1 08.03.2024 GerBI Community Meeting 2 The scientific motivation: •FAIR data: research data management, especially for image data is challenging due to the complexity of the data type; tools, standards, infrastructure have to be developed •however, RDM is crucial for the application of AI, for data integration, for economic (re-)use of data, for increasing the releability of data, for sustainability< Why? The community motivation: •RDM is requested by imaging core facility users, by research institutions, funders and journals •German OMERO user group was founded back in 2017, today known as the RDM4mic group, which is open to all •In 2018, DFG launched the National Research Data Infrastructure (NFDI), GerBI-GMB was invited (by DFG) to participate. 08.03.2024 GerBI Community Meeting 3 The motivation for GerBI as a scientific society: •RDM projects are usually designed beyond the boundaries of a single institute •they should be aligned with international communities and projects •RDM projects often require research software development, these positions are outside the public sector pay scale, e.g. subcontracting is a usual mode of operation Why? ➢benefits for GerBI are: •a significant contribution to the sustainability of the society by the third party funding •active role in shaping the emerging RDM landscape (tools, standards, infrastructure) ➢GerBI as a scientific society provides well established, but flexible infrastructures, based on a solid community of experts in the field, embedded in the international community 08.03.2024 GerBI Community Meeting 4 Why: Josh and the Next Generation File Format Images: “!dam uploads” & “Navid zooms” by Henning Falk, ©2022 NumFOCUS, is used under a CC BY 4.0 license DFG NDFI4BIOIMAGE March 2023 – 2028 PI SWP, Josh Moore GerBI RDM Projects w/ funding –an overview 08.03.2024 GerBI Community Meeting 5 Wellcome Leap Delta Tissue 2021Aug. 2024 PI Josh Moore CZI EOSS5 June 2022Oct. 2024 PI Josh Moore CZI Single Cell May 2023Oct. 2024 PI Josh Moore 2021 2022 2023 2024 EU Horizon foundingGIDE 2024 – 2026 PI Josh Moore Host: CZI Neubias March 2023 – Feb 2025 PI Robert Haase ∑ > 1 Mio; € 08.03.2024 GerBI Community Meeting 6 •Wellcome Leap DeltaTissue: •MARFA - Master Research Funding Agreement - between WL and GerBI, supported by FieldFisher lawyer team •Third Party Funding Bank Account at VR Bank Konstanz •DFG NFDI4BIOIMAGE: •GerBI membership of the NFDI society (NFDI Verein) •GerBI Guideline for the use of project overheads („Leitlinie zur Verwendung der Programmpauschale“) •CZI Single Cell: •GerBI template for Agreement on the forwarding of a grant („Muster für Mittelweiterleitungsvertrag“), supported by FieldFisher •EU Horizon FoundingGIDE: •GerBI Gender Equality Plan (GEP) GerBI 3rd party funding infrastructure 08.03.2024 GerBI Community Meeting 7 GerBI‘s road to NFDI •May 2018: DFG launches the National Research Data Infrastructure, GerBI-GMB is invited (by DFG) to participate. •June 2019: GerBI-GMB votes for submission of a Letter of Intent for a consortium for bioimage data management within the NFDI at the 4th General Assembly in Brno, ELMI meeting •August 2019: internal call for interested partners both for NFDI and for a smaller DFG proposal in the alternative funding line „Information Infrastructures for Research Data“ •July 2020: Submission of updated LoI to 2nd NFDI Call in 2020 •October 2020: Submission of DFG proposal „I3D:bio; Information Infrastructure for BioImage Data“ Applicants: Konstanz, Osnabrück, Düsseldorf, Freiburg. 34 Letters of Support from: RDM4mic and GerBI-GMB members, Leibniz “Health !lliance”, NFDI consortia, companies. •November 2020: Uni Konstanz provides a position for an NFDI coordinator (→ Christian Schmidt) 08.03.2024 GerBI Community Meeting 8 GerBI‘s road to NFDI •December 2020: internal call for interested partners for NFDI •July 2021: DFG approval of „I3D:bio; Information Infrastructure for BioImage Data“ project •July 2021: Binding Letter of Intent for a consortium for bioimage data management within NFDI •November 2021: NFDI4BIOIMAGE proposal submission for the 3rd round of NFDI consortia •January 2022: Start of I3D:bio project •February 2022: Online assessment of the 3rd round NFDI consortia •June 2022: Funding recommendation for NFDI4BIOIMAGE (7/16 proposals recommended) •November 2022: Funding approval for NFDI4BIOIMAGE by BMBF •March 2023: Start of NFDI4BIOIMAGE and I3D:bio RDM team at TiM2023 08.03.20249 I3D:bio RDM team at TiM 2023 •The I3D:bio project aims to improve FAIR image data management: tools, metadata standards, training<; •The project is focusing on OMERO as a image data base which is widely spread in the community Let‘s setup a TiM2023-OMERO and make all TiM image data FAIR FAIR: Findable – Accessible – Interoperable – Reusable GerBI Community Meeting Community Meeting 2024 04.03.2024 1 6 Technology Development / Goal Package your data for sharing (with permission) ★ that are machine readable ★★★ in consistent containers ★★★★ to enable science. ★★★★★ including descriptive labels ★★ Images generated by Andra Waagmeester & Josh Moore through AI generation using Midjourney (Sep. 2023) Center of Excellence Community Meeting 2024 04.03.2024 1 7 Technology Development / Goal Metadata Data Community Meeting 2024 04.03.2024 1 8 Technology Development / NGFF Chunkable file format Monolithic file format SPLIT CONCATENATE NETWORK NETWORK Access via network External data storageLocal computer Susanne Kunis 2022-2024 Open Science that are machine readable ★★★ Community Meeting 2024 04.03.2024 1 9 Technology Development / SpatialData 2023-2025 Single Cell Luca Marconato Giovanni Palla Isaac Virshup Kevin A. Yamauchi that are machine readable ★★★ Community Meeting 2024 04.03.2024 2 0 Technology Development / Linked Data A $55M PROGRAM Delta Tissue INTEGRATED PLATFORMS FOR PREDICTING CHANGES IN TISSUE STATE https://wellcomeleap.org/delta-tissue/ Andra Waagmeester that are machine readable ★★★ 2021-2024 Community Meeting 2024 04.03.2024 2 1 Technology Development / Linked Data “Adrie JC Steyn, Africa Health Research Institute Assaf Zaritsky, Ben-Gurion University of the Negev Gunnar Carlsson, BlueLightAI, Inc. Michael Roukes, California Institute of Technology Chris Sander, Harvard Medical School Fabian Theis, Helmholtz Zentrum München Maddy Parsons, King’s College London Simon Fredriksson, Pixelgen Technologies Shankar Subramaniam, University of California San Diego Greg Hannon, University of Cambridge Virginie Rozot, University of Cape Town Denise Kirschner, University of Michigan Medical School Hagan Bayley, University of Oxford Omer Bayraktar, Wellcome Sanger Institute Stéphane Pagès, Wyss Center for Bio and Neuroengineering Joerg Bewersdorf, Yale University A new platform – a ‘tissue time machine’ – that can profile tissue states and predict transitions between states (‘Delta Tissue’ or ‘ΔT’). The platform would provide quantitative, multi-scale, multimodal information sufficient to build integrated prediction models of key cell and tissue states and transitions. Andra Waagmeester that are machine readable ★★★ 2021-2024 Community Meeting 2024 04.03.2024 2 2 Technology Development / GIDE (Global Image Data Ecosystem) Matthew Hartley Shuichi Onami 2024-2026 in consistent containers ★★★★ Community Meeting 2024 04.03.2024 2 3 Technology Development / FAIR-IO in consistent containers ★★★★ Susanne Kunis Stefanie Weidtkamp-Peters Elisa May 2023-2028 Community Meeting 2024 04.03.2024 2 4 Technology Development / Beyond to enable science. ★★★★★ Roland Nitschke Caterina Strambio De Castillia Community Meeting 2024 04.03.2024 2 5 Tech Development / Getting involved https://gerbi-gmb.de/teams/image-data-analysis-management/ 04.03.2024 GerBI Community Meeting 5 Why metadata? Schmidt C, Hanne J, Moore J et al. Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey [version 2; peer review: 2 approved]. F1000Research 2022, 11:638 (https://doi.org/10.12688/f1000research.121714.2) PMID: 36405555, CC-BY 4.0 (http://creativecommons.org/licenses/by/4.0) •Expertise - MDEmic (Susanne) •Quarep-LiMi (Roland and many GerBI members) •GerBI contributed to REMBI (Nadine) •Metadata is essential for FAIR bioimaging data Metadata guidelines and tools are requested → Explore user tools, how to change habits, and the needs to make metadata FAIR 04.03.2024 GerBI Community Meeting 6 Tangible results from I3D:bio for the community www.i3dbio.de 04.03.2024 GerBI Community Meeting 7 Use Case DKFZ Heidelberg Reusable training material requested by the RDM4mic group (2022) 04.03.2024 GerBI Community Meeting 8 Tangible results from I3D:bio for the community 04.03.2024 GerBI Community Meeting 9 Tangible results from I3D:bio for the community •Optimized annotation strategies for image analysis (Tom) •Contributions to the software source code and best practices for OMERO integration with Fiji (Tom & Michele) •Improving OMERO.web & OMERO.figure (Tom) https://www.youtube.com/watch?v=BNZKMiuK7kg&list=PL2k-L-zWPoR7SHjG1HhDIwLZj0MB_stlU&index=14 04.03.2024 GerBI Community Meeting 10 Use Case TU Dresden Medical Faculty CFCI •AxioScan was purchased. Concept: start using OMERO with the new system •How and where to start? •Steps: •Discussing system requirements and examples of installations (T. Zobel, S. Kunis) •The request to install OMERO on the TU Dresden Medical Faculty IT servers was granted in May 2022 •Training: OMERO server and command line usage for CF staff (Tom Boissonnet, June 2022) •Testing of OMERO at CFCI (pilot phase with slidescanner and EM data) •Discussing special data types and research use cases: How to handle data organization and annotation in OMERO? (TiM 2023) •Preparing data for analysis and publication (August 2023, I3D:bio and NFDI4BIOIMAGE) •First research paper published with REMBI-annotated bioimages in the public group of OMERO at TU Dresden Medical Faculty CFCI •Jannasch et al. (2024), APL Mater, https://doi.org/10.1063/5.0182672 •Next steps: •Rolling out to more users, enabling seamless data analysis in connection with OMERO 04.03.2024 GerBI Community Meeting 11 NFDI4BIOIMAGE Data Stewardship Team 2 2 2 co-applicant institutions (Task Area Leaders) participating institutions community use cases data stewards (DaSts) IT IT IT IT infrastructure (storage & playground: @WWU & @ALU-FR) •20+ FTE to work on practical RDM solutions and training •help desk for emerging RDM issues •close collaboration with other NFDI consortia •Collaborate with Industry (via Quarep-LiMi & others) But not: a central data archive for all bioimaging data Modified after: Stefanie Weidtkamp-Peters. (2023, Juni 22). NFDI4BIOIMAGE - National Research Data Infrastructure for Microscopy and BioImage Analysis - Online Kick-Off 2023. Zenodo. https://doi.org/10.5281/zenodo.8070038 04.03.2024 GerBI Community Meeting 12 NFDI4BIOIMAGE Data Stewardship Team https://nfdi4bioimage.de 04.03.2024 GerBI Community Meeting 13 Christian Schmidt Scientific Project Manager Project Coordinator of I3D:bio Networking and Outreach Coordinator of NFDI4BIOIMAGE GerBI member since 2022 Meet us at our poster! https://zenodo.org/doi/10.5281/zenodo.10805203