These templates were developed on the basis of the NEON and AWI protocol templates, and adapted for the purpose of capturing metagenomic ocean observing workflows.
These templates were developed by the Better Biomolecular Ocean Practices (BeBOP) group coming 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 or pdfs). To allow the community to understand differences in practices and the potential for integrating the data generated using the BOPs, we offer the means of standardization via the development of protocol templates. These allow us to more efficiently log and compare protocols at scale.
This repository currently contains protocol templates for the following steps of an omics observation:
All protocol templates follow a similar structure: General metadata on top, followed by sections on background, personnel required, and equipment required. Next, you will find a section on the Standard Operating Procedure (SOP), which should be used to report on the exact steps taken as part of executing a protocol. In the template for insilico analysis, in place of the SOP, there is a Guide to the archived methodology and a section on Archive content. The templates conclude with References and Appendices.
Note, that the protocol-level metadata is to be reported as part of the protocol in the section [TO_BE_ADDED] following the Minimum Information about an Omic Protocol (MIOP). For more information and guidance on MIOP, please consult the MIOP repository in this organisation.
To use the templates and apply them to your own protocols Please fork this repository For guidance on how to fork a repository, please see here.
In the forked repository, you may then freely edit the content sections of the protocol in markdown. If you are unfamiliar with markdown language, please see this list of resources and softwares to support your work:
Training resources
Markdown Editors (not necessary, but may facilitate editing in markdown)
For the versioning of your protocol, please note the section on version control in the Towards a Best Practice for Developing Best Practices in Ocean Observation (BP4BP): Supporting Methodological Evolution through Actionable Documentation publication.
As noted there, we recommend the use of semantic versioning.
Given a version number MAJOR.MINOR.PATCH, increment the:
- MAJOR version when you make incompatible API changes
- MINOR version when you add functionality in a backwards compatible manner
- PATCH version when you make backwards compatible bug fixes
Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
For sharing the protocols, PDF versions of the protocols may be more convenient(xRef https://github.com/BeBOP-OBON/0_protocol_collection_template/issues/1). The PDF versions of the protocols can also be added to your repository alongside with their markdown versions.
Please see below for some tools to convert your markdown file to PDF
For information on creating a release of your repository and getting DOIs from Zenodo, please see the guidance here.
Please also note the GLOMICON community on Zenodo. When archiving your repository with Zenodo, please do so in this community.
Please use this GitHub repository’s Issue tracker to request changes/additions or report errors or specific concerns related to the protocol templates.