Vae infra

[jburel]

Introduce a new page with info about the infra used
and display existing notebooks

[sbesson]

Now deployed at https://snoopycrimecop.github.io/idr.openmicroscopy.org/analysis-environments.html for initial review

[pwalczysko]

The layout seems to be dictated by the thumbnail sizes which vary. Is it possible in the first iteration to either omit the thumbnails or put them under the texts and badges, so that these do not "float/jump" from item to item ?

Actually, clicking on the thumbnails in the section

I am thinking that for this particualr section (Generic notebooks) it is confusing to point to single particular studies by means of links under the displayed thumbnails. I would get rid of the thumbs completely for this section, also, the first thumb is actually pointing to the webclient, not to the gallery search, which is confusing. This thumb should be replaced by explanatory text/link, something like "run this from the IDR user interface".

[sbesson]

Deployed at https://snoopycrimecop.github.io/idr.openmicroscopy.org/analysis-environments.html.

The new page title makes complete sense and reflects out transition away from a single Virtual Analysis Environment that we deploy into a set of external Analysis Environments

I am a bit confused by the semantics. We use the terms Notebooks and Apps but there is no Apps sub-section but a Tools one instead. I assume App currently refers to the single Shiny R app? And Tools are the ones described in ITR?

The notebooks classification is also slightly confusing. The first section is about study-specific notebook but all the notebooks from the last section are also study-specific. Is the issue is that every item has effectively multiple categories (notebook vs app, language/tool, study-specific vs cross-study) and we are trying to build human-readable categories based on a combination of these elements like the gallery headings?

Outside the additions of this PR, my biggest question is the relationship with the content of https://idr.openmicroscopy.org/about/itr.html. For instance several notebooks are duplicated in both locations and maintained in two separate JSON files. Also the "Using tools to explore IDR" section displays the same notebook as the ones that pop up when clicking on N in ITR.
Having different views on the same data is okay if they serve the readabaility but we might want to think on how to maintain and potentially libnk both sections.

Minor comments:

• the link to idr-notebooks is the only one that does not load a notebook. Possibly each notebook could have its own entry in the future
• I am still not overly sold on the proposed layout within JSON. It definitely does the job and expresses the hierarchy but I could imagine moving away from WebPage/breadcrumb in the future.

Despite all the issues pointed out above, we currently have a lot of broken links which should be addressed asap and getting these concepts is a complex task that will take several iterations. My inclination is to agree on a working starting point that can go live as part of the next prod release, capture outstanding improvements/discussions as issues and work on it iteratively.

[jburel]

To discuss options next Monday during the IDR call

The points to discuss are about the notebooks sections.

• The First section is for the notebooks/apps (Shiny) specific to a study i.e. explore the results associated to the study and presented by the authors. This could be include in gallery to allow "search for notebooks/apps" similar to what we do for Authors, gene. and an icon could be added to the results found
• The second section is for "generic notebooks" i.e. using the various APIs like idr-py. This is not attached to any specific study or tools. It explores the data in IDR e.g. compounds, genetophenotypes
• The third section is for notebooks using a tools listed in ITR. Some of that could be a review of ITR. and/or could follow the same approach that the notebooks of the first section. In that case we will need to introduce annotation for the tool used to allow a search

[will-moore]

A couple of first-impression comments...

• The heading subtitle: "IDR uses Analysis Environments provided..." is jumping the gun a bit. Page intro should be "This page provides sample analysis routines for working with the data in IDR" etc before going into details of how it is provided.
• I would probably expect the "generic" IDR-wide examples to come before the study-specific examples, since they would have a wider audience?
• I tried one notebook: "Access Images and metadata using omero-py". The focus in this one is actually on s3 rather than omero-py. It could do with a bit of explanation about how only a small number of IDR images are available as OME-Zarr on s3, which these are (blog post) and that more are planned. The notebook worked fine, except the Z-slider on the final image had no effect for me.

[jburel]

@will-moore: The initial goal is to migrate some of the content from IDR analysis. Since we now rely on public resources or resources run by EBI, the text has been adjusted.
The second part with example is the key point of the discussion. Do we want to have it here? A few options are proposed, in "gallery-idr" view is one for some notebooks.
We need a redirect in place for the next IDR release to avoid broken links.

[jburel]

Notebooks discussions moved to
#144

[will-moore]

I have been looking at this PR as a basis for adding an Analyse Data section to the IDR front page.
I would like to provide a small number of well described notebooks that lead a user from into -> more advanced.
But I am struggling to find a notebook that gives a nice intro to Python OMERO API.

E.g. https://colab.research.google.com/github/ome/omero-guide-python/ lists lots of examples, but they all ask for passwords for workshop server?

https://mybinder.org/v2/gh/ome/omero-guide-r/HEAD?filepath=notebooks/idr0021_Segmentation-noSave.ipynb is fine for R.
Something like this in Python would be great.

https://mybinder.org/v2/gh/ome/omero-guide-python/HEAD?filepath=notebooks/idr0062_prediction_zarr_public_s3.ipynb is using OME-NGFF which is nice to have somewhere, but not as a general intro since it is limited to pre-converted data.

https://colab.research.google.com/github/IDR/idr-notebooks/ also gives a big list of notebooks, making it hard for the novice user to know which one to pick.

I don't know if this section of the front page should be more like a brief omero-guide: 1) try this, 2) now try this... or if it should briefly describe the Analysis options then link to a different page?

[jburel]

I don't really like the idr-notebooks repository. It is a collection of notebooks. Some of related to paper, some not really useful.
I started to extract some to other repos but I had to put that work on hold

• https://mybinder.org/v2/gh/ome/omero-guide-r/HEAD?filepath=notebooks/idr0021_Segmentation-noSave.ipynb is fine for R. Yes agree
  This should be no difficult.
• https://colab.research.google.com/github/ome/omero-guide-python/ lists lots of examples, but they all ask for passwords for workshop server?
  We have a few that are not workshop specific but should certainly extend the coverage.