Better Biomolecular Ocean Practices (BeBOP) is a UN Ocean Decade project under the Ocean Biomolecular Observing Network (OBON) programme. This project developed out of the Task Team 21-03: Omics/eDNA Protocol Management under the Ocean Best Practices System.
We aim to achieve increased comparability between Biomolecular Ocean Practices (BOPs). Currently, the wealth of ocean biomolecular practices is shared in diverse formats (e.g. text in publications, pdfs, ...). To better compare differences in practices and integrate data generated using BOPs, we developed markdown templates as well as standardized metadata describing protocols (called Minimum Information about an Omics Protocol or "MIOP"). Our goal is to create machine-readable protocol documents where changes can be tracked, assigned DOIs, and linked to associated datasets. These tools will also allow us to compare protocols at scale and make protocols more findable.
Note
Our 2021 paper describes our overall vision and organizational principles:
Samuel, Robyn M., et al. "Toward a global public repository of community protocols to encourage best practices in biomolecular ocean observing and research." Frontiers in Marine Science 8 (2021): 758694. https://doi.org/10.3389/fmars.2021.758694
You can share your protocols on Github following the instructions below or we also have a location to share protocols on protocols.io: https://www.protocols.io/workspaces/better-biomolecular-ocean-practices-bebop
Navigate to our template repository
On the main page of this repository:
- Above the file list, click Use this template.
- Select Create a new repository.
- Choose repository ownership (select BeBOP-OBON to be featured on the BeBOP page) and name your repository after your project or institution
- You can always link your repository later to the BeBOP-OBON github space if you would like to work on protocols within your own github location first.
Note
For further guidance on how to create your own repository from this template please see here.
In your new repository, you may then freely edit the content sections of our protocol templates in markdown.
Tip
If you are unfamiliar with markdown language, please see this list of resources and softwares to support your work:
Training resources
- Markdown Cheatsheet by Adam Pritchard
- Markdown Crash Course by Traversy Media
- Writing on GitHub by GitHub docs
Markdown Editors (not necessary, but may facilitate editing in markdown)
- Visiual Studio Code
- MacDown, open source Markdown editor for macOS
In each protocol template, we begin with a table of metadata fields that will help us sort and organize protocols. In the future, this will enable us to create a better mechanism for discovering new protocols.
Please fill out the MIOP terms and use this document as a guide (included in the template repository): MIOP_definition.md
If you have any feedback or suggestions about our templates please post an issue on the template repository or about MIOP fields in our miop repository. We also welcome contributions of new types of templates to our collection. Our goal is to cover protocols ranging from study initiation to data sharing, across an entire omics workflow.
