2022_08_17_SeedSeq (cpg0018)

[shntnu]

Segmentation/ Feature extraction has already been performed Profile creation has already been performed Data can be public in RODA Immediately

Update as generated:
[Link to profile repo]
[Link to publication repo]
cpg0018

• [ ] Metadata completely filled out in Project Profiler Database (Imaging Platform internal use only)
• [x] Segmentation/Feature extraction complete
• [x] Profiling complete

Transfer to CellPainting Gallery:

• [ ] Upload data to RODA (is private by default)
• [ ] Run validation script to ensure completion
• [ ] Update cellpainting-gallery/README.md
• [ ] Make RODA entry public

If data is being published, prepare for publication:

• [ ] Run Distributed-BioFormats2Raw to create .ome.zarr files
• [ ] Upload (meta)data to IDR (images remain hosted in cellpainting-gallery).

Once published:

• [ ] Make IDR entry public
• [ ] Update cellpainting-gallery/README.md and open-data-registry/cellpainting-gallery.yml to reflect publication
• [ ] Move this Issue from cellpainting-gallery-private to cellpainting-gallery. This step can be performed at an earlier point if it needs inputs from an external collaborator.

[bethac07]

Airtable Profiling Experiment tag (and links to other data) is TA RNAi.

The paper only has per-well mean profiles, do we think there is a chance that the raw analysis files and/or backends live anywhere? If so, "In the imaging-platform bucket in the TA folder" is not their location.

[shntnu]

The paper only has per-well mean profiles, do we think there is a chance that the raw analysis files and/or backends live anywhere?

This was the MySQL / BatchProfiler era, so nope :)

For our reference, this is the project wiki: https://www.ipwiki.app/Z_Paper_on_seed_effects_confounding_RNAi_image-based_profiling (no action needed)

[bethac07]

Oh, I bet I know where they are - I bet they are in s3://imaging-platform-cold/imgdb/imgdb02/2011_07_13_TargetAccelerator-backup.gz

[shntnu]

Oh, I bet I know where they are - I bet they are in s3://imaging-platform-cold/imgdb/imgdb02/2011_07_13_TargetAccelerator-backup.gz

Those will be SQL dumps though

[bethac07]

Those will be SQL dumps though

Yup, but if we want to associate the analysis files, do we have another option for how to get them? I naively assumed we would only want things in the gallery with single-cell analysis (or at least non-normalized per-well analysis), but maybe not?

[shntnu]

Yup, but if we want to associate the analysis files, do we have another option for how to get them? I naively assumed we would only want things in the gallery with single-cell analysis (or at least non-normalized per-well analysis), but maybe not?

Good point. I think we put it in regardless because it will still be useful for the community and, at minimum, will be an incentive to someday get the rest of the (single cell) data.

e.g. https://github.com/carpenterlab/2017_goldsborough_mlcb/issues/1#issuecomment-1149039103

[bdiazroh]

The images are ready to transfer from the imaging-platform bucket, but it seems I don't have permissions to to the transfer, I asked Erin to initiate the transfer with her credentials but she also does't have the permissions. Once Shantanu gives either one of us the permissions we can upload data to RODA. And the other thing is the descriptor of the data set. Is it cpg0018-RNAi? or cpg0018_RNAi-cellpainting?

[shntnu]

We are all set to proceed with the transfer.

@bdiazroh this might still need Beth or Erin to do the transfer. I will discuss in Slack

For my notes: this is in https://github.com/jump-cellpainting/cellpainting-gallery-config/pull/27

The descriptor is cpg0018-singh-seedseq

@bdiazroh we maintain a full listing of public and currently embargoed dataset identifiers here https://github.com/broadinstitute/cellpainting-gallery-private#datasets

[bethac07]

So to be clear, the final path should be (under the bucket) cpg0018-singh-seedseq/broad/images/some_batch_name/images/, with then the folders, right? Any requests for the batch name @shntnu? I can initiate a transfer to that location once confirmed.

[shntnu]

So to be clear, the final path should be (under the bucket) cpg0018-singh-seedseq/broad/images/some_batch_name/images/, with then the folders, right?

Correct - thanks for double-checking

Any requests for the batch name @shntnu? I can initiate a transfer to that location once confirmed.

I could not find the creation date, so I'd go with something anodyne: batch1

[bethac07]

@bdiazroh had already nicely organized everything with a batch name of Batch1, so that's how we go :)

Due to permissions disparities, this is going to be a two step sync, but step 1 is underway!

[bethac07]

Sync 1 is done, and currently deleting from source 1. Sync 2 seems to have permissions issues on the cellpainting-gallery end, discussing in linked Slack discussion

[bethac07]

Sync 2 done!