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saezlab / scverse_hackathon

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User story: offline access #5

Open grst opened 1 year ago

grst commented 1 year ago

I work on a hardened HPC with no internet connection whatsoever. It should be possible for my systems administrators to place the annotation database at a central location such that it can be accessed by all users.

The "installation" of the reference database should be easy enough that a user can do it on their own, if the systems administrators are not willing to provide a central installation (i.e. ideally flatfiles that are copied somewhere).

E.g. 

# Download the database from somewhere
wget https://exampe.com/annotation_db.sqlite

# Copy the database via secure connection onto the HPC
scp annotation_db.sqlite hpc:data/annotation_db.sqlite

To use the database

annotation_pkg.set_cache_dir("/home/sturm/data/annotation_db.sqlite")
slobentanzer commented 1 year ago

is annotation_pkg the prior knowledge resource?

grst commented 1 year ago

It would be the package that provides the user-friendly API for annotation (i.e. the package we intend to build)

slobentanzer commented 1 year ago

gotcha. we should definitely create some more detailed user stories in the meeting next week, to explicitly define the features we need.

slobentanzer commented 1 year ago

Maybe the guys from Jan Baumbachs lab can help here. We will work on a solution for "federated data", to be used in tandem with their federated learning approaches (featurecloud.ai), which also requires encapsulation.