Giters

broadinstitute / cellpainting-gallery

Cell Painting Gallery

Home Page:https://broadinstitute.github.io/cellpainting-gallery/

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

2018_05_30_ResistanceMechanisms_Kapoor (cpg0028)

shntnu opened this issue · comments

commented

Segmentation/ Feature extraction is being performed by Cimini lab (done)
Profile creation is being performed by Carpenter-Singh lab (done)
Data can be public in RODA Immediately

Update as generated:

Link to profile repo (same as publication repo): https://github.com/broadinstitute/profiling-resistance-mechanisms/tree/master/0.generate-profiles/profiles
Link to publication repo: https://github.com/broadinstitute/profiling-resistance-mechanisms
cellpainting-gallery identifier: cpg0028-kelley-resistance

  • Metadata collection form filled out by collaborator or Imaging Platform member (https://airtable.com/shrVxz9DcoMlDoCBI)
  • Metadata completely filled out in Project Profiler Database (Imaging Platform internal use only)
  • Segmentation/Feature extraction complete
  • Profiling complete

Transfer to CellPainting Gallery:

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.
commented
  • make s3://imaging-platform/projects/2018_05_30_ResistanceMechanisms_Kapoor/ publicly accessible (for now) to simplify the process
  • run python restore_intelligent.py imaging-platform projects/2018_05_30_ResistanceMechanisms_Kapoor to thaw ("restore") the files
  • Create issue in https://github.com/broadinstitute/cellpainting-gallery/issues/
commented

@gwaybio

The final folder structure should look like this https://github.com/broadinstitute/cellpainting-gallery/blob/main/folder_structure.md

We need someone to provide the aws s3 sync instructions to copy the files over to s3://cellpainting-gallery. I've started a stub here https://github.com/broadinstitute/profiling-resistance-mechanisms/blob/cpg-upload/scripts/cpg_upload.sh (borrowing from https://github.com/broadinstitute/cellpainting-gallery/blob/main/upload.md#uploading-multiple-plates-at-once)

We can tag team between you, me, @mekelley and @yhan8 to get this done.

Any thoughts on how to get going on this?

commented

Thanks @shntnu - just now seeing this post.

I don't know how we could get going on this. Is this something you can handle (maybe looping in Yu)? We could get Dave on this, but I fear it would only take you longer to explain than to do

commented

I can transfer files to cpg. @gwaybio can you clarify - should I transfer all data or only batches larger than a certain number?
For reference, for other datasets in the cellpainting-gallery we are including all data (including pilots) even if they are not in the final publication.

commented

Very grateful, @ErinWeisbart !!

should I transfer all data or only batches larger than a certain number?
For reference, for other datasets in the cellpainting-gallery we are including all data (including pilots) even if they are not in the final publication.

Megan had some notes here broadinstitute/profiling-resistance-mechanisms#122 (comment) where she linked to a spreadsheet indicating the batches to upload.

I like the idea of uploading everything.

Do you need any more information, @ErinWeisbart ?

commented

Thank you @ErinWeisbart !! 🙏

commented

I will go ahead and upload all, since it sounds like nobody objects. Don't think I need more info but will re-ping if I hit any stumbling blocks.