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SBRG / pymodulon

Python package for analyzing and visualizing iModulons
MIT License
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Add ica_data objects for published datasets #38

Closed avsastry closed 3 years ago

avsastry commented 3 years ago

We should add tar.gz files for E. coli, B. subtilis, and S. aureus to a folder in the root directory called published_data.

sapoudel commented 3 years ago

Should we do zipped json file? Or tar all the relevant files?

avsastry commented 3 years ago

Sorry, zipped json file for easy import

kevin-rychel commented 3 years ago

I think a zipped json sounds best, right?

On Tue, Nov 17, 2020 at 9:23 AM Saugat Poudel notifications@github.com wrote:

Should we do zipped json file? Or tar all the relevant files?

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sapoudel commented 3 years ago

Also, would if make more sense to host the json file on imodulondb have the front page of github point to it? Idk how big these files are but we dont want to make the repo too big. What do you think?

kevin-rychel commented 3 years ago

I think the size can determine that. I definitely think they should be added to imodulondb, and then we can include them here too if the zipping keeps them small enough?

Is pymodulon public, so imodulondb users could use it to parse the jsons? If so I'll add a brief section to my about page to link to the GitHub.

On Tue, Nov 17, 2020 at 9:25 AM Saugat Poudel notifications@github.com wrote:

Also, would if make more sense to host the json file on imodulondb have the front page of github point to it? Idk how big these files are but we dont want to make the repo too big. What do you think?

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avsastry commented 3 years ago

pymodulon is not ready to be public just yet.

I agree they should be on iModulonDB though. Perhaps we should just make a new repo called imodulon_objects?

avsastry commented 3 years ago

The three published iModulons are now in this package as part of the example data. Future iModulons will not be bundled in this package, but rather in a different repo or on iModulonDB

https://github.com/SBRG/pymodulon/tree/master/src/pymodulon/data/objects