Landscape analysis before we start working on this project

[malvikasharan]

As mentioned by Lisanna Paladin in #1, we should collect resources important for landscape analysis here.

These resources can be a combination of references we want to use in the development of the training materials, existing materials (cc-by or similar free license) that can be reused or linked, as well as examples of resources that have not been effective at supporting novice learners.

[Lisanna]

The Carpentries resources

General:

• Genomics Lessons
• Ecology Lessons

Specifically relevant to Open Biosciences:

• Introduction to Conda for (Data) Scientists
• Introduction to Bioinformatics workflows with Nextflow and nf-core
• Getting Started with Snakemake
• Snakemake for Bioinformatics
• Reproducible computational environments using containers: Introduction to Singularity

Cyverse resources

• Foundations of Open Science Skills 2021

[malvikasharan]

(Also see: Markowetz, F. (2017). All biology is computational biology. PLoS Biol., 15(3), e2002050. doi: 10.1371/journal.pbio.2002050).

[Lisanna]

EOSC-Pillar RDM training catalogue, potentially anything here is relevant (The Turing Way is listed there)

[malvikasharan]

Going through the list of current incubators, here a a few projects that deal with ML already that we should connect with and reuse

• https://carpentries-incubator.github.io/ml4bio-workshop/
• https://carpentries-incubator.github.io/machine-learning-novice-python/
• https://carpentries-incubator.github.io/machine-learning-novice-sklearn/
• http://datascibc.org/Data-Science-for-Docs/
• https://carpentries-incubator.github.io/machine-learning-librarians-archivists/
• https://carpentries-incubator.github.io/bioc-intro/

Packaging and publishing

• https://carpentries-incubator.github.io/introduction-to-conda-for-data-scientists/
• https://carpentries-incubator.github.io/python-packaging-publishing/

different levels of cloud computing and HPC training materials

• http://www.hpc-carpentry.org/
• https://carpentries-incubator.github.io/hpc-intro/