# Bioinformatics (20) ## BHG2023-OMERO-ARC Andrea Schrader, Michele Bortolomeazzi, Niraj Kandpal, Torsten Stöter, Kevin Schneider, Peter Zentis, Josh Moore, Jeam-Marie Burel, Tom Boissonnet Licensed CC-BY-4.0 Repository for documentation during the 2nd de.NBI BioHackathon Germany - 11.-15.12.2023 - OMERO-ARC project (in short: BHG2023-OMERO-ARC) Tags: Nfdi4Bioimage, Bioinformatics, OMERO, Exclude From Dalia Content type: Github Repository [https://github.com/NFDI4BIOIMAGE/BHG2023-OMERO-ARC](https://github.com/NFDI4BIOIMAGE/BHG2023-OMERO-ARC) --- ## Best practice data life cycle approaches for the life sciences Philippa C. Griffin, Jyoti Khadake, Kate S. LeMay, Suzanna E. Lewis, Sandra Orchard, et al. Published 2018-06-04 Licensed UNKNOWN The authors provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on ‘omics’ datasets and computer-based data processing and analysis. Tags: Bioinformatics, Reproducibility, Research Data Management, Sharing, Open Science, Include In Dalia Content type: Publication [https://doi.org/10.12688/f1000research.12344.2](https://doi.org/10.12688/f1000research.12344.2) --- ## Bio.tools database Licensed CC-BY-4.0 Tags: Bioinformatics, Exclude From Dalia Content type: Collection [https://bio.tools/](https://bio.tools/) --- ## CytoVI Deep generative modeling of antibody-based single cell technologies Florian Ingelfinger, Nathan Levy, Can Ergen, Artemy Bakulin, Alexander Becker, Pierre Boyeau, Martin Kim, Diana Ditz, Jan Dirks, Jonas Maaskola, Tobias Wertheimer, Robert Zeiser, Corinne C. Widmer, Ido Amit, Nir Yosef Published 2025-09-12 Licensed CC-BY-4.0 CytoVI is a probabilistic generative model that enables statistically rigorous and integrative analysis of antibody-based single cell technologies, outperforming existing methods and enabling key functionalities like cell embeddings and differential protein expression testing, with applications in B cell maturation, non-Hodgkin lymphoma, and diagnostic flow cytometry. Tags: Artificial Intelligence, Bioinformatics, Include In Dalia Content type: Preprint [https://www.biorxiv.org/content/10.1101/2025.09.07.674699v1](https://www.biorxiv.org/content/10.1101/2025.09.07.674699v1) --- ## DL4Proteins-notebooks Michael Chungyoun, Courtney Thomas, Britnie Carpentier, GabeAu79, puv-sreev, Jeffrey Gray Published 2024-09-04T12:24:24+00:00 Colab Notebooks covering deep learning tools for biomolecular structure prediction and design Tags: Bioinformatics, Exclude From Dalia Content type: Github Repository, Collection [https://github.com/Graylab/DL4Proteins-notebooks](https://github.com/Graylab/DL4Proteins-notebooks) --- ## Democratizing knowledge representation with BioCypher Sebastian Lobentanzer, Patrick Aloy, Jan Baumbach, Balazs Bohar, Vincent Carey, Pornpimol Charoentong, Katharina Danhauser, Tunca Doğan, Johann Dreo, Ian Dunham, Elias Farr, Adrià Fernandez-Torras, Benjamin Gyori, Michael Hartung, Charles Tapley Hoyt, Christoph Klein, Tamas Korcsmaros, Andreas Maier, Matthias Mann, David Ochoa, Elena Pareja-Lorente, Ferdinand Popp, Martin Preusse, Niklas Probul, Benno Schwikowski, Bünyamin Sen, Maximilian Strauss, Denes Turei, Erva Ulusoy, Dagmar Waltemath, Judith Wodke, Julio Saez-Rodriguez Published 2023-06-19 Licensed UNKNOWN BioCypher is a framework to support users in creating KGs Tags: Knowledge Graph, Bioinformatics, Exclude From Dalia Content type: Publication [https://www.nature.com/articles/s41587-023-01848-y](https://www.nature.com/articles/s41587-023-01848-y) --- ## EMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data Jullia Jakiela, Laura Cooper, Katarzyna Kamieniecka, Krzysztof Poterlowicz Published 2025-02-05 Licensed CC-BY-4.0 INTERNATIONAL The objective is to organise bioimage metadata, find out what REMBI is and why it is useful, categorise what metadata belongs to each of the submodules of REMBI and gather the metadata for an example bioimage dataset. Tags: Bioinformatics, Bioimage Analysis, Include In Dalia Content type: Tutorial [https://training.galaxyproject.org/training-material/topics/imaging/tutorials/bioimage-REMBI/tutorial.html](https://training.galaxyproject.org/training-material/topics/imaging/tutorials/bioimage-REMBI/tutorial.html) --- ## EMBL-EBI material collection EMBL-EBI Licensed CC0 (MOSTLY, BUT CAN DIFFER DEPENDING ON RESOURCE) Online tutorial and webinar library, designed and delivered by EMBL-EBI experts Tags: Bioinformatics, Exclude From Dalia Content type: Collection [https://www.ebi.ac.uk/training/on-demand?facets=type:Course%20materials&query=](https://www.ebi.ac.uk/training/on-demand?facets=type:Course%20materials&query=) --- ## Galaxy Imaging Galaxy Team Licensed ['ACADEMIC FREE LICENSE VERSION 3.0', 'CREATIVE COMMONS ATTRIBUTION 3.0 (CC BY 3.0) LICENSE'] Galaxy is an open source tool that offers a filtered set of tools that you can assemble into workflows to manage image data, and perform image analysis and processing. Tags: Galaxy, Bioinformatics, Exclude From Dalia Content type: Tool [https://imaging.usegalaxy.eu](https://imaging.usegalaxy.eu) --- ## GalaxyProject YouTube Channel Galaxy Team Published 2020-06-16 Licensed UNKNOWN Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational research. Tags: Galaxy, Bioinformatics, Exclude From Dalia Content type: Youtube Channel [https://www.youtube.com/c/galaxyproject](https://www.youtube.com/c/galaxyproject) --- ## Get started accessing the de.NBI cloud. de.NBI Licensed UNKNOWN Tutorial for accessing de.NBI cloud Tags: Bioinformatics, Cloud Computing, Exclude From Dalia Content type: Tutorial [https://cloud.denbi.de/get-started/](https://cloud.denbi.de/get-started/) --- ## Lecture-materials of the DeepLife course Carl Herrmann, annavonbachmann, David Hoksza, Martin Schätz, Dario Malchiodi, jnguyenvan, Britta Velten, Elodie Laine, JanaBraunger, barwil Published 2023-12-06 Licensed UNKNOWN Tags: Bioinformatics, Exclude From Dalia Content type: Github Repository, Slides, Notebook [https://github.com/deeplife4eu/Lecture-materials/](https://github.com/deeplife4eu/Lecture-materials/) --- ## TESS Event database Tags: Bioinformatics, Exclude From Dalia Content type: Collection, Event [https://tess.elixir-europe.org/events](https://tess.elixir-europe.org/events) --- ## TESS training materials Licensed UNKNOWN Tags: Bioinformatics, Exclude From Dalia Content type: Collection [https://tess.elixir-europe.org/materials](https://tess.elixir-europe.org/materials) --- ## Ten simple rules for making training materials FAIR Leyla Garcia, Bérénice Batut, Melissa L. Burke, Mateusz Kuzak, Fotis Psomopoulos, et al. Published 2020-05-21 Licensed CC-BY-4.0 The authors offer trainers some simple rules, to help make their training materials FAIR, enabling others to find, (re)use, and adapt them. Tags: Metadata, Bioinformatics, FAIR-Principles, Include In Dalia Content type: Publication [https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854) --- ## Tracking of mitochondria and capturing mitoflashes Leonid Kostrykin, Diana Chiang Jurado Published 2024-11-20 Licensed CC-BY-4.0 Tags: Bioinformatics, Bioimage Analysis, Include In Dalia Content type: Workflow, Tutorial [https://training.galaxyproject.org/training-material/topics/imaging/tutorials/detection-of-mitoflashes/tutorial.html#tracking-of-mitochondria-and-capturing-mitoflashes](https://training.galaxyproject.org/training-material/topics/imaging/tutorials/detection-of-mitoflashes/tutorial.html#tracking-of-mitochondria-and-capturing-mitoflashes) --- ## WorkflowHub Stian Soiland-Reyes, Finn Bacall, Bert Droesbeke, Alan R Williams, Johan Gustafsson, et al. Licensed BSD-3-CLAUSE A registry for describing, sharing and publishing scientific computational workflows. Tags: Bioinformatics, Workflow, Workflow Engine, Python, R, Exclude From Dalia Content type: Collection [https://workflowhub.eu/](https://workflowhub.eu/) --- ## de.NBI YouTube Channel de.NBI Published 2015-08-28 Licensed UNKNOWN The de.NBI (German Network for Bioformatics Infrastructure) Youtube channel (http://www.denbi.de/) Tags: Bioinformatics, Exclude From Dalia Content type: Youtube Channel [https://www.youtube.com/@denbi5170](https://www.youtube.com/@denbi5170) --- ## de.NBI cloud access registration guide de.NBI Published 2024-11-04 Licensed UNKNOWN Tutorial for registering for de.NBI cloud access Tags: Bioinformatics, Cloud Computing, Exclude From Dalia Content type: Tutorial [https://cloud.denbi.de/wiki/registration/](https://cloud.denbi.de/wiki/registration/) --- ## deNBI Online Training Media Library de.NBI Licensed UNKNOWN The de.NBI (German Network for Bioformatics Infrastructure) Online Training & Media Library provides a collection of training materials for bioinformatics and computational biology. Tags: Bioinformatics, Galaxy, Exclude From Dalia Content type: Website [https://www.denbi.de/online-training-media-library](https://www.denbi.de/online-training-media-library) ---