New OceanGliders Chla SOP?

[soerenthomsen]

This is copied over from the intro thread:

@sophieclayton wrote:

[soerenthomsen]

Hi @sophieclayton thanks for connecting here! This is great! :)

So far we are not planing to develop a full chlorophyll SOP but there has been some work by members of the OceanGlider Community to write a 2 pager. Maybe it makes sense to connect these efforts towards a full SOP? Happy to provide the contacts. For sure OceanGliders would be glad to support such a process.

Concerning oxygen please let your colleagues know that they are welcome to join the Oxygen SOP to make it even better.

Thanks a lot
Soeren

[sophieclayton]

As you are rearranging things, now seems like a good time to follow up! I think that it would be great to pull together some folks to push for a full CHL SOP.

Franky Lane @flane00 is working on chl data from Slocum gliders right now and he will (hopefully) share his QA/QC pipeline in the next couple of months.

Last week I co-lead a workshop at WHOI aimed at developing best practices for using OOI BGC sensor data and although we didn't get into the details of dealing with glider data, we did start to discuss them.

We hope to open up the OOI best practices for review at the end of the summer, will keep this group posted!

[soerenthomsen]

Hi @sophieclayton thanks for following up! Indeed it would be great to unit forces here.
So far we have no OceanGliders Chla_SOP but would like to co-develop one with your people!

What we have so far is a quiet developed DMQC 2 pager overview piece, which could be build on.
So far not on GitHub though. It is lead by:
Filipa Carvalho (@pipa85), Sandy Thomalla , Thomas Ryan-Keogh (@tjryankeogh), Tom Hull (@tomhull), Soeren Thomsen, Bastien Queste (@bastienqueste)

I think it would be key to try to not reinvent the wheel nor duplicate efforts here.
OceanGliders is very much interested in converging/co-develop Best Practices with your OOI efforts to make them sustainable and global.

i.e. We could setup a joint Chla SOP GitHub repo as we did for the others if that is supported by OOI? Using Jupyter books etc to make it inclusive and open and easily updatable. As we could clone the existing ones this takes just a few hours and I am happy to show how this works.

[sophieclayton]

@soerenthomsen Agree that we should not duplicate efforts. For the OOI best practices we have stopped short of addressing glider specific issues in detail.
My suggestion would be to keep the SOPs separate, but to pool expertise and build the glider CHL SOP on what we have already been doing for OOI.
@pipa85 @alisonpchase @hipalevsky what are your thoughts?

[soerenthomsen]

I have a few questions before I take more time/days to think and make a longer thoughtful answer.

Is it possible for everyone to join the OOI SOPs you are developing? Is it open for any other networks, individuals or institutes to join / co-author?

The aim of OceanGliders is to support global harmonisation and reduce fragmentation. i.e. it is possible to endorse OceanGliders SOPs if they get implemented in regional networks or institutions. Is that possible for an OOI SOP?

The challenge with Best Practices is not that there are no documents/papers out but more that we need to converge them. This is what I learned having worked the last 2 years on this topic. So avoiding to have 2 new SOPs and try to keep each of them "alive" would be a success in my view. Especially knowing how much work of many individuals the 4 OceanGliders SOPs were. So having 2 new SOPs dilutes the effort and reduces the chances to hit a critical mass needed to sustain and maintain the SOPs. We ask people to put a lot of their time into this. So we have to avoid to work in parallel as much as possible.

I cannot speak for OceanGliders here alone but my feeling is that we should try to manage to write one joint new SOP. Building on yours if that is progressed and add what has been done by people like @pipa85 @tjryankeogh et al. related to DMQC.

@ptestor @vturpin please engage and outline your vision and how we could support convergence.

@catsch (BGC ARGO) please engage in this important discussion and maybe share ARGO experience on convergence

Jay Pearlman (on GitHub?) and @jkarstensen maybe you can add the OBPS perspective? You also said OBPS has a process to support convergence Is that correct?

[ptestor]

I agree the added value of OceanGliders SOPs comes from the convergence process. I feel the community would very much like to see the development of an OceanGliders SOP on chl-a that would be developed internationally and result from a convergence process. Then, and added value is that it could be relatively easily endorsed by GOOS. We do not want to duplicate efforts and the will institutions/projects to develop best practices is understandable but I would like to insist we need to work on BP convergence, adoption and endorsement if we want these best practices development efforts to be most useful.

[jkarstensen]

still - convergence across Europe for specific observations (e.g. MSFD framework) do also make sense. The set of EOVs for European needs is more comprehensive then it is for GOOS. Such BP may receive "only" an endorsement by the future GROMM RI or the EuroGOOS TT or whatever is the sustained body for Europe.

[sophieclayton]

For clarity: the OOI BGC best practices and user guide is a network-specific guide that outlines OOI network-specific context and operational information and then gives best practices for four sub-groups of sensors found on that network's arrays: bio-optics, oxygen, carbonate chemistry and nitrate.

The OOI BGC effort is fundamentally different to the OceanGlidersCommunity SOPs as it is a single document that gives broader best practices applicable to a larger set of sensors deployed on a range of platforms (e.g. fixed depth moorings, profiler moorings, gliders). So my sense is that there is a strong case to point to the OceanGlidersCommunity SOPs from the OOI BGC best practices to give users the more specific info needed if they are most interested in the OOI glider data (and we have already added such links to our working document).

We are probably 6-12 months behind the OceanGlidersCommunity in terms of development of the OOI BGC best practices, but our intent is similar. We have had a round of internal review, then a round of review by beta testers, and last week convened an in person workshop at WHOI to discuss revisions. We aim to open the best practices guide to community review in 2-3 months' time and follow the steps for GOOS endorsement.

All of that to say that the OOI group is not engaged in developing a full glider-specific chl SOP and so there would not be a duplication of efforts. I won't speak for others in the group, but I would like to see a full glider chl SOP developed and would be happy to be involved (and I imagine that such an SOP would be cited and linked to from the more general OOI BGC best practices).

@hipalevsky should chime in here too.

[soerenthomsen]

Thanks for clarifying!

[ptestor]

Yes thanks and it looks like a great plan! :-)

[hipalevsky]

Thanks @sophieclayton for connecting what we're doing with the OOI best practices and user guide with this great effort on the OceanGliders SOPs. Thanks @soerenthomsen for leading this and to everyone involved. @pipa85 is in our OOI BGC working group and had brought this effort to our attention earlier on in the process, and it's great to have this as a model and example. As @sophieclayton described, our scope is quite different, so rather than a duplication of effort I agree that these are synergistic in that we will be able to cite the OceanGliders SOPs within our best practices and user guide.

[FiIipaCarvalho]

Sorry I’ve been away and are just now trying to catch up on emails.
I agree with @sophieclayton and @hipalevsky. The scope of the OOI document is very different and actually does very little with gliders specifically.
In line with the thoroughness of the oxygen SOP, the chl SOP should stand alone.
We can bring some glider/profiler people from the working group to contribute to this side effort. we can also bring some of the background info on bio-optics researched for the OOI cookbook - as you say, no need to re-invent the wheel.

[catsch]

I will be happy to contribute to glider CHLA SOP

[tjryankeogh]

I also support a global SOP for Glide Chl-a and I am happy to contribute towards it.

[soerenthomsen]

Great to see so many interested in moving this forward! Please tell others who are interested to join too.

To get it started we would need two (better 3) who are willing to co-lead this effort.

I can clone the oxygen repo (which is a template repo) for you and change everything to make it work for Chla and look the same for Chla. Does this sound reasonable? But we need some leads :)

[soerenthomsen]

Agree especially thinking of the fact that we will also include the data processing at the Data Centers etc. This is better to have clearly separated per variable to keep it easy for the operators.

All overlaps can be simply linked in the documents as everything is online anyhow here.

[tjryankeogh]

I am also happy to help co-lead with @pipa85. I agree that it would make sense to keep CHLA and BBP separate, to take into account different sensor types.

[callumrollo]

I don't have a great amount of chla experience, but I'm happy to take responsibility for the technical side of things keeping the jupyter-book working and reviewing PRs

[sophieclayton]

@pipa85 @soerenthomsen @catsch @tjryankeogh If we are mostly trying to target the SOPs to EOVs rather than sensor types, so i would suggest we split into a CHLa SOP and potentially a particle SOP that could include optical and acoustic backscatter.
Thoughts?

[soerenthomsen]

Yes this makes sense! Let's start with Chla_SOP for now to stay in line with the OceanGliders and GOOS EOV approach etc

[soerenthomsen]

Next steps:

• 1) I will clone the oxygen SOP repo and adapt everything to from oxygen_* to chla_* -> Done https://github.com/OceanGlidersCommunity/Chla_SOP

• 2) We might have to make a quick training with everyone who does not feel 100 % secure with GitHub. @callumrollo just told me that he will offer a 30 min training for everyone. This is in particular key for the lead authors who have to govern the document.

• 3) Will assign admin, write rights etc. This will be based on already existing work in the framework of OOI and the OceanGliders DMQC chapter which was also lead by @pipa85 or?

• 4) Start to work on the SOP

Anything missing?

[MOchiara]

Hi all! I have some experience in chlorophyll data processing, QC and calibration from glider data and I would happy to contribute

[sophieclayton]

wonderful! great to have you onboard!

[soerenthomsen]

Thanks everyone this is great! I transferred our discussion in the new Chla_SOP repo!

@sophieclayton @pipa85 @catsch @callumrollo @MOchiara et al