So, it looks like we didn't use the main branch as we were thinking (documented in CONTRIBUTING.md).

I'm thinking we should make the gh-pages branch the default for this repository. It will make contributing easier and allow us to see more details on how the repo might be used (in the insights section). Other than the binder environment file (which didn't work all that great to begin with - and it could be copied to gh-pages) there is no other purpose for main.

I can make gh-pages the default, but should we delete main?

Before TDWG we need to update the citation file. Maybe push to zenodo and get a DOI too?

I've seen some warning pop up that we should probably look at. I don't think it's a requirement to fix asap, per se.

https://github.com/ioos/bio_mobilization_workshop/actions/runs/4449218838

build-website

Node.js 12 actions are deprecated. Please update the following actions to use Node.js 16: actions/setup-python@v2. For more information see: https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/.

build-website

The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/

Create environment files which can be picked up by Binder to spin up a Python or R environment, if folks have trouble locally.

• Python
• R
• Do we want a combined environment like the IOOS conda env?

The datasets in https://github.com/ioos/bio_data_guide/tree/main/datasets can be linked to as examples where needed. Specifically the example_* ones could be useful. I am not sure where it makes sense to put those links.

We also have information in https://ioos.github.io/bio_mobilization_workshop/about/

It would be helpful if we added this information to one of those pages.

What this workshop will cover:

• Darwin Core and the required terms for OBIS and GBIF.
• Typical data cleaning tasks needed to standardize the data.
• Getting your data into a final Darwin Core format.
• Common QA/QC steps, data enhancement, and validation tools.
• Required metadata information.
• How to get your data into the Integrated Publishing Toolkit.
• Tools that will help in all of the above processes.

The goal is that by the end of the workshop you will have a dataset in a final standardized state and shared to OBIS. We are hoping to address some of the blockers that you identified, including: lack of time, training, and specific formatting questions.

We have a short time together therefore our focus will be hands-on work in breakout rooms using the dataset you bring to the workshop. We will not have many presentations and they will be relatively short. Instead we will have large portions of time for you to work on your data and ask questions when you hit a stumbling block. Therefore, if you do not have a dataset to work on you may not find this workshop a good use of your time.

What this workshop will not cover:

• What is OBIS?
• Rationale for sharing data with OBIS.
• Using data that’s already in OBIS.

If you would like to learn more about OBIS and a short rationale for sharing data to it, please watch this two minute video and this two minute video and share them with those you want to work with to share data.

Section 4 should reflect the title that we have updated it to: "Metadata, QA/QC, and publishing". I tried to edit this myself on the main page but I think it's actually pulling from the URLs? Or at least I couldn't figure out where the text was to update it.

This repo is primarily for hosting the website deployed from the gh-pages branch. Do we even need main anymore?

I think we can get the mybinder stuff to work from gh-pages.

Need to create the extras page then add content

moved from #24

If we continue to get folks to provide some boilerplate info on the dataset they plan to work on. Maybe we can make breakout rooms topical based on data types, instead of lesson pages. Eg. passive acoustic, edna, survey, trawl, etc.

Just thinking of other ways the breakout rooms could be more engaging...

We should include a page(?) on where to continue having the discussions after the workshop.

Need to think about where to put it?

The readme has a bunch of information we don't necessarily need anymore.

Let's clean this up to only contain the pertinent information:

• Title
• Description
  • What do we want to use main for? According to CONTRIBUTING we were hoping to have folks upload their data/code. Is that still the case?
  • I think How this repo is organized should be in the description/readme.
• mybinder environment links
• Link to the workshop website: https://ioos.github.io/bio_mobilization_workshop/

Let's keep it clear and consise.

Link for Post-workshop help & survey (https://ioos.github.io/bio_mobilization_workshop/07-post-workshop/index.html) should be to https://ioos.github.io/bio_mobilization_workshop/08-post-workshop/index.html

• GBIF DwC Vadlidator
• Search NERC

https://ioos.github.io/bio_mobilization_workshop/03-data-cleaning/index.html

Page https://ioos.github.io/bio_mobilization_workshop/08-post-workshop/index.html

Add https://classroom.oceanteacher.org/

https://ioos.github.io/bio_mobilization_workshop/06-qa-qc/index.html

CoC points to carpentries to report. As we're not officially carpentries, we should have another mechanism to report.

https://ioos.github.io/bio_mobilization_workshop/CODE_OF_CONDUCT.html

2023 is now complete. We should tag the website materials. I think zenodo will automatically mint a new doi for a new version, but also provide a collection DOI for all versions (link).

Zenodo archives your repository and issues a new DOI each time you create a new GitHub release. Follow the steps at "Managing releases in a repository" to create a new one.

For example,

• https://doi.org/10.5281/zenodo.7401979 - cite all versions
• https://doi.org/10.5281/zenodo.7401980 - cite just 2022

Also, I wonder if there is a way to add the .html files to the release. Just thinking in case jekyll disappears we wouldn't be able to rebuild the website again. If we drop the .html files in as assets to the release, folks would be able to pull those up in a browser. Just not sure if those will be pulled over to the zenodo DOI package.

https://ioos.github.io/bio_mobilization_workshop/01-introduction/index.html

from Carolina Peralta:

Some questions are placed in first personal pronoun (I) and others are in second person (you). I suggest to standardize (Did this workshop help me move past the blockers I identified?; How comfortable are you with aligning data to Darwin Core?) Maybe use all questions with "I" personal pronoun?

Survey form is editable in gforms. Let me know if you need edit access granted.

I want to create .md files that give an overview & relevant links for the topics and exercises listed in the agenda.

OBIS has some?

copied from #24

Create better descriptions of the breakout rooms so people know what room to go to ask their question.

Right now we are using The Carpentries Lesson template. @albenson-usgs shared that there is The Carpentries Workshop template.

To do this we need to:

• Compare workshop template with lesson template to identify differences
• Copy out the markdown files we've made/edited
• replace all files with workshop template files
• replace appropriate markdown files (from above)
• update README, CONTRIBUTING, etc.

          add example check for `individualCount` as it should be an integer.

Originally posted by @MathewBiddle in #57 (comment)

Hi

I am just scheming through the pages for the workshop and noticed some information that may have outdated. I don't know what the original information should be, so I could not submit a pull request for the Darwin Core and Extension Schemas page

Occurrence Core + extensions

Using the occurrence core plus relevant extensions means that you can capture more of the data that’s been recorded.

The link https://tools.gbif.org/dwca-validator/extensions.do now points to the new data validator login page, but not the extensions

In the occurrence extension table, row basisOfRecord:

Pick from these controlled vocabulary terms: HumanObservation, MachineObservation, PreservedSpecimen, LivingSpecimen, FossilSpecimen

There are more vocabularies for basisOfRecord (e.g. MaterialSample)

from #24

Make sure to ask for country in the pre-workshop survey

Now that we know we will be doing it again, we should update the landing page to include dates and other relevant information.

• pre-workshop survey: https://docs.google.com/forms/d/e/1FAIpQLSeLsNrcwfU2EGtObf_E97juI55LZGR2Fc8VsPpTSpRmXG7ufA/viewform?usp=sf_link

Participants likely have management applications/successes/failures to share.

How can we capture this information in a way that could be used in the motivation section of future proposals?

Do we want statistics like "75% of participants reported that this workshop will help them achieve goal X"?

https://ioos.github.io/bio_mobilization_workshop/04-create-schema/index.html

https://ioos.github.io/bio_mobilization_workshop/setup.html

Do we want to put anything in the setup page for the workshop?

Typically this contains information on how to install software packages required for the lesson. See Software Carpentry R setup page. I think adding a section for RStudio and a section for Python would be helpful for those who stumble upon the site.

from Naomi:

rather than just in the playlist so that video and writeup are together on one page

I'd like to have a DOI for this repo.

TODO:

• Create a release
• tag said release
• mint doi through Zenodo
• update citation.cff

review the Continuing the Conversation page and update with new post-survey once we have it.

We have a couple examples to borrow from:

• https://github.com/ocean-tracking-network/2021-04-13-act-workshop/tree/gh-pages
• https://ocean-tracking-network.github.io/dfo-bio-robis-exercise/
• https://github.com/k-rns/workshop_data_reuse/tree/gh-pages
  • https://k-rns.github.io/workshop_data_reuse/

@albenson-usgs mentioned that we don't have citations for the comics presented in the workshop. Fortunately, we are only providing the links in the markdown files and letting jekyll do the rendering for the website. But, we should be adding a citation underneath each of the images to appropriately cite xkcd.

From https://xkcd.com/about/:

Note: You are welcome to reprint occasional comics pretty much anywhere (presentations, papers, blogs with ads, etc). If you're not outright merchandizing, you're probably fine. Just be sure to attribute the comic to xkcd.com.

moved from #24

Keeping in mind we don't want to ask too many questions- next time do we want to ask for ratings on the different sections so we can figure out which ones need improvement.

I propose we change this repository name to bio_mobilization_workshop.

Oceanhackweek had a nice approach of using the active gh-pages branch for the current year. Once the year is complete, move the content to a new branch that indicates the year (eg. 2022_site). Then work on/update the gh-pages branch for the next iteration of the workshop.

We can do something similar for main as well to preserve the datasets/code that were worked on that year. Give the branch a name like 2022_main.

I would like this to be somewhat futureproof in that we can use it for other workshops we might want to host in the future.

What happened to our discussions about a certification of sorts?

Can we create some PDF that we send folks after the workshop to say they attended? A certification of attendance...

moved from #24

Should we make the workshop longer (a full week?) to build in GTKY/ networking time?

Build time takes a bit to publish site updates (~3 mins). We probably don't need all the RMarkdown stuff...

Say we were to hold this workshop again, how can we host the different workshops materials so they are available online?

I think Oceanhackweek did some neat tricks to make this happen?

cc: @ocefpaf

https://ioos.github.io/bio_mobilization_workshop/07-validation-and-publishing/index.html

Anyone have a favicon they want to use? For the browser tab and header of the webpage.

IOOS has a couple here

The existing favicons (for the carpentries) can be found here https://github.com/ioos/bio_mobilization_workshop/tree/gh-pages/assets/favicons

To do

• create/decide on a favicon
• make a new directory (bmw?) and add our favicons to it.
• update _config.yml to reference new directory

Error message: Error during build: .0.0 is not valid SemVer string

I think it has to do with not specifying the r-base version number in environment.yml. However, if we specify r-base version than the rstudio option doesn't work 😵‍💫

I'll do some tinkering and see what we can do.

File: coverconcepcionspecies_matched.txt

Section on website:

link to the required terms table on the Intro to Darwin Core page. Link should be something like

[link]({{ page.root }}/01-introduction/index.html#what-are-the-required-darwin-core-terms-for-publishing-to-obis)

Error: Unable to resolve action `r-lib/actions@master`, unable to find version `master`

https://github.com/ioos/bio_mobilization_workshop/actions/runs/3321475196/jobs/5489169194