Collections

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.

Open Work Flow Articles (OWFAs)

This is an inclusive collection of workflows related to biodiversity and ecology (especially non-microbial). A big portion covers genome assembly of newly-sequenced species, using long reads (ONT or PacBio HiFi), possibly complemented by chromosome capture (typically HiC) for scaffolding, or/and by short reads (typically Illumina). It also aims at collating workflows related to ecology, biodiversity, biogeography, natural history, and related scientific areas, across the whole WorkflowHub and ...