Collections

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

• Repeat masking
• RNAseq QC and read trimming
• Find transcripts
• Combine transcripts
• Extract transcripts
• Fgenesh annotation

Update May 2026: Note: The "convert formats" workflow (880) is now no longer needed.

Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation, and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work ...

Example showing how to interact with the public bioimaging resources like the Image Data Resource (IDR)

Collection of de-novo genome assembly workflows written for implementation in Galaxy

Input data should be PacBio HiFi or ONT long reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads

Executing all workflows will output two scaffolded haplotype assemblies and the complete QC analyses

Please run the workflows in order: WF0 (there are for long reads and for Illumina HiC), WF1, WF2, WF3 (optional), WF4

Collection of EC-Earth3 workflows running with Autosubmit 3, with and without task wrappers, for different Slurm-based HPC platforms. See the individual descriptions for further details.

Collections of materials used as part of the Data Steward Curriculum

https://github.com/crim-ca/application-packages

Common Workflow Language definitions that can be employed in the context of OGC API - Processes deployment. Open Geospatial Consortium (OGC) API Processes can leverage CWL to integrate worklows and processes.

Open source Web API bridging OGC API - Processes with CWL by the Computer Research Institute of Montreal / Centre de recherche informatique de Montréal (CRIM): https://github.com/crim-ca/weaver

Collection of workflows exploring data in the Image Data Resource (IDR).

Collection of workflows used or developed by the EuroScienceGateway project.