Training (12)#

DataPLANT knowledge base#

Published 2022-12-14

Licensed CC-BY-4.0

Explore fundamental topics on research data management (RDM), how DataPLANT implements these aspects to support plant researchers with RDM tools and services, read guides and manuals or search for some teaching materials.

Tags: Research Data Management, Training, Dataplant

Content type: Collection

https://nfdi4plants.org/nfdi4plants.knowledgebase/index.html


Docker Mastery - with Kubernetes + Swarm from a Docker Captain#

Bret Fisher

Licensed UNKNOWN

In this course you will learn how to use Docker, Compose and Kubernetes on your machine for better software building and testing.

Tags: Docker, Training

Content type: Videos, Tutorial, Online Course

https://www.udemy.com/course/docker-mastery/?srsltid=AfmBOornR5gRqOg-4v8Nsap1z24CaPPUPxg8JzyqEGZ6MvW_dh-sf4Af&couponCode=ST2MT110724BNEW


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, Training

Content type: Collection

https://www.ebi.ac.uk/training/on-demand?facets=type:Course%20materials&query=


Glencoe Software Webinars#

Chris Allan, Emil Rozbicki

Licensed UNKNOWN

Example Workflows / usage of the Glencoe Software.

Tags: OMERO, Training

Content type: Videos, Tutorial, Collection

https://www.glencoesoftware.com/media/webinars/


I2K 2024: clEsperanto - GPU-Accelerated Image Processing Library#

Stephane Rigaud, Robert Haase

Licensed BSD-3-CLAUSE

Course and material for the clEsperanto workshop presented at I2K 2024 @ Human Technopol (Milan, Italy). The workshop is an hands-on demo of the clesperanto project, focussing on how to use the library for users who want use GPU-acceleration for their Image Processing pipeline.

Tags: Clesperanto, Training, Bioimage Analysis, Notebooks, Workflow

Content type: Github Repository, Workshop, Tutorial, Notebook

StRigaud/clesperanto_workshop_I2K24


I2K2024 workshop material - Lazy Parallel Processing and Visualization of Large Data with ImgLib2, BigDataViewer, the N5-API, and Spark#

Stephan Saalfeld, Tobias Pietzsch

Published None

Licensed APACHE-2.0

Tags: Training

Content type: Workshop, Notebook, Github Repository

https://saalfeldlab.github.io/i2k2024-lazy-workshop/

saalfeldlab/i2k2024-lazy-workshop


Image Processing with Python#

Mark Meysenburg, Toby Hodges, Dominik Kutra, Erin Becker, David Palmquist, et al.

Licensed CC-BY-4.0

This lesson shows how to use Python and scikit-image to do basic image processing.

Tags: Segmentation, Bioimage Analysis, Training, Python, Scikit-Image, Image Segmentation

Content type: Tutorial, Workflow

https://datacarpentry.org/image-processing/key-points.html


Object Tracking and Track Analysis using TrackMate and CellTracksColab#

Joanna Pylvänäinen

Published None

Licensed GPL-3.0

I2K 2024 workshop materials for “Object Tracking and Track Analysis using TrackMate and CellTracksColab”

Tags: Bioimage Analysis, Training

Content type: Github Repository, Tutorial, Workshop, Slides

CellMigrationLab/I2K_2024


SWC/GCNU Software Skills#

Licensed CC-BY-4.0

Computational skills training at the UCL Sainsbury Wellcome Centre and Gatsby Computational Neuroscience Unit, delivered by members of the Neuroinformatics Unit.

Tags: Training

Content type: Collection, Online Course, Videos, Tutorial

https://software-skills.neuroinformatics.dev/index.html


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, Training

Content type: Publication

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854


Ultrack I2K 2024 Workshop Materials#

Jordão Bragantini, Teun Huijben

Licensed BSD3-CLAUSE

Tags: Segmentation, Bioimage Analysis, Training

Content type: Workshop, Github Repository, Tutorial

royerlab/ultrack-i2k2024

https://royerlab.github.io/ultrack-i2k2024/


Using Glittr.org to find, compare and re-use online training materials#

Geert van Geest, Yann Haefliger, Monique Zahn-Zabal, Patricia M. Palagi

Licensed CC-BY-4.0

Glittr.org is a platform that aggregates and indexes training materials on computational life sciences from public git repositories, making it easier for users to find, compare, and analyze these resources based on various metrics. By providing insights into the availability of materials, collaboration patterns, and licensing practices, Glittr.org supports adherence to the FAIR principles, benefiting the broader life sciences community.

Tags: Training, Bioimage Analysis, Research Data Management

Content type: Publication, Preprint

https://www.biorxiv.org/content/10.1101/2024.08.20.608021v1