I found this document from February 2025 with some feedback on the BeBOP templates. Some of it is probably not relevant anymore or was resolved, but I wanted to capture it here. We can close the issue if/when everything is addressed.
Updated BeBOP Template Feedback
Main Question: When people publish these protocols, do we want them to delete the instructions or keep them in there? Or are they just a template thing?
All Templates
● New “Related Protocols’ is a bit confusing. What happens when there are no related external protocols or internal protocols - should we advise people to leave these sections blank or delete them? That would be the benefit of a singular section, as it was in the original template, with simply a column to denote whether it was external or internal.
○ The release date of the external protocol is important and should not be excluded. These protocols might not always be on GitHub, so seeing the access date might not provide as much information as we’d like.
● Under Background - Replace with “This document describes the required protocol to conduct [insert name of the method/protocol]”
● Under Spatial coverage - No link associated with “For regional term guidance, see here”
Sampling Template
● In the Equipment section, is the note about the Opentrons Robot consumables necessary for sampling?
● Might be worth it to list Preparations as a separate heading and not just a subheading of sampling. Especially for eDNA sampling, preparations can be quite extensive and have different stages. Ours for eDNA Niskin sampling are lengthy, and they would benefit from not being clumped into this section.
○ Might be worth it to do this for all templates for consistency
● Storage might benefit from the same subheading size as quality control and basic troubleshooting as it has long term implications - don’t want it getting lost under sampling
PCR Template
● The related protocols section doesn’t match the other templates. The underlined header and extra table are a remnant from the original template and need to be deleted.
● No definitive place for positive control information. It is important to include these sequences and rationale for selecting them.
DNA Extraction Template
● No corrections besides ones noted in “All Templates”
I found this document from February 2025 with some feedback on the BeBOP templates. Some of it is probably not relevant anymore or was resolved, but I wanted to capture it here. We can close the issue if/when everything is addressed.
Updated BeBOP Template Feedback
Main Question: When people publish these protocols, do we want them to delete the instructions or keep them in there? Or are they just a template thing?
All Templates
● New “Related Protocols’ is a bit confusing. What happens when there are no related external protocols or internal protocols - should we advise people to leave these sections blank or delete them? That would be the benefit of a singular section, as it was in the original template, with simply a column to denote whether it was external or internal.
○ The release date of the external protocol is important and should not be excluded. These protocols might not always be on GitHub, so seeing the access date might not provide as much information as we’d like.
● Under Background - Replace with “This document describes the required protocol to conduct [insert name of the method/protocol]”
● Under Spatial coverage - No link associated with “For regional term guidance, see here”
Sampling Template
● In the Equipment section, is the note about the Opentrons Robot consumables necessary for sampling?
● Might be worth it to list Preparations as a separate heading and not just a subheading of sampling. Especially for eDNA sampling, preparations can be quite extensive and have different stages. Ours for eDNA Niskin sampling are lengthy, and they would benefit from not being clumped into this section.
○ Might be worth it to do this for all templates for consistency
● Storage might benefit from the same subheading size as quality control and basic troubleshooting as it has long term implications - don’t want it getting lost under sampling
PCR Template
● The related protocols section doesn’t match the other templates. The underlined header and extra table are a remnant from the original template and need to be deleted.
● No definitive place for positive control information. It is important to include these sequences and rationale for selecting them.
DNA Extraction Template
● No corrections besides ones noted in “All Templates”