The NBIS Support Framework (NBIS-SF) is about creating a collaborative framework for NBIS support projects and the related data management plans. The idea is to have a common framework and knowledge-base that NBIS experts may choose to adopt and expand as they perform support-related work. This includes tools for reproducibility (e.g. Conda, Snakemake, Docker), version control (git, GitHub), information required to be in NBIS reports and report templates (e.g. RMarkdown, LaTeX, KnitR, Jupyter), as well as support-related information (data management guidelines, consultation guidelines, contract templates, etc.). NBIS also has a separate repository for pipelines, which you can find at NBISweden/pipelines. For more information regarding working reproducibly in NBIS, please check out the NBIS course Tools for Reproducible Research.
You can find more complete examples and inspiration of how to work reproducibly in NBIS support work at the following places:
- Mahesh's NBIS project template
- Erik's NBIS project template
- Roy's R Markdown templates
- Erik's NBIS Quarto template
- NBIS Assembly project template
- Rasmus' project template
- Cormac's peer review track project template
- Cookiecutter Data Science
First create a new repository for your project by using NBIS-SF as a template. You can do this directly from the NBIS-SF GitHub by pressing the "Use this template" button and select "Create new repository". This will take you through the creation of your new repo like normal, but it will contain all the content currently available on NBIS-SF in a single, initial commit. Set the Owner to NBISweden.
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For user-fee projects, name your new repository with NBIS, the Redmine issue number, the year, plus a descriptive name, e.g. NBIS-4412-18-mast. You can then clone your new repository like you would normally.
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For peer-review projects, name your new repository with NBIS followed by the WABI ID of the project. The WABI ID is comprised of the PI's first name initial(s), the PI's surname, and the year and month (YYMM) of the application deadline. For example: NBIS-M_Bergö_1305
Note
If you don't know the WABI ID for the project, you can ask your manager or search for the project in Redmine. The Redmine issue for the project should have a field "WABI ID" containing the ID.
By default repositories are public, meaning they are accessible to anyone on the Internet. In case, you want to restrict access to the repo to inside NBIS only:
- While creating repo choose "Private"
- Go to repository "Settings" -> "Collaborators and Teams" -> search field in "Manage Access" and type "Staff"
- Give appropriate access to "Staff" team (Read, Write, Triage etc.) and voilá, now all at NBIS have access
All contributions are welcome, small and large! The central idea behind NBIS-SF is to develop an up-to-date framework for NBIS support projects, to share knowledge and to streamline common bioinformatics tasks. Anybody working at NBIS is welcome to contribute! If you want to contribute something, please see the CONTRIBUTING.md file.
Questions and feedback can be sent to Erik Fasterius, Olga Dethlefsen or John Sundh.