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
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
Bio.tools database#
Licensed CC-BY-4.0
Tags: Bioinformatics, Exclude From Dalia
Content type: Collection
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
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
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
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
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
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
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
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
TESS Event database#
Tags: Bioinformatics, Exclude From Dalia
Content type: Collection, Event
TESS training materials#
Licensed UNKNOWN
Tags: Bioinformatics, Exclude From Dalia
Content type: Collection
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
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
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
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
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