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

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


Bio.tools database#

Licensed CC-BY-4.0

Tags: Bioinformatics, Exclude From Dalia

Content type: Collection

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


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

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



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=


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


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


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/


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

deeplife4eu/Lecture-materials


TESS Event database#

Tags: Bioinformatics, Exclude From Dalia

Content type: Collection, Event

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


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


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


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/


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


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/


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