dondi / GRNsight

Web app and service for modeling and visualizing gene regulatory networks.
http://dondi.github.io/GRNsight
BSD 3-Clause "New" or "Revised" License
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Add PPI demo #1065

Closed dondi closed 7 months ago

dondi commented 7 months ago

For parity with GRNs, we need to add PPI demos to the app. @kdahlquist will generate the file and this can be added to the app in the same way that the existing demos are added.

dondi commented 7 months ago

We’ll start with an export based on the database then move on to Dr. Dabir’s data when ready

kdahlquist commented 7 months ago

Demo #5 PPI Network (Yeastmine - SGD 2023-03-29; 18 proteins, 81 edges).xlsx

I created this network from the database. It is all the proteins that interact with Aim32p, which is the protein that Dr. Dabir studies.

I exported it from GRNsight and then modified the filename.

It has only a "network" sheet. I changed the text in cell A1 to read "protein 1/protein 2".

It loads back into GRNsight OK, but currently, it loads as a GRN, not PPI because there's nothing to tell GRNsight that it is a PPI network.

In doing this, I think I uncovered a bug, but will report in a different issue.

kdahlquist commented 7 months ago

I'm open to shortening the filename to something like:

Demo #5 PPI (18 proteins, 81 edges)

"Network" is probably redundant. If we shorten it this way, we lose the provenance of the data, but that could be put into the documentation. This could be better due to readability in the dropdown menu.

dondi commented 7 months ago

File is ready to go—we will use the content of cell A1 to determine the Network Mode to switch to, as noted in #1066. Label the demo as noted in the comment above

Demos are encoded directly as JSON objects; the easiest way to convert is probably to temporarily add a console.log to the code which displays the converted network object. When opening the file, this network JSON will appear in the Developer Console and can then be transcribed to the source code in demo-workbooks.js

As noted, we will use cell A1 of the Network sheet to determine the Network Mode. Further, we will need to adjust the warning to adapt to these changes

kdahlquist commented 7 months ago

Verified present in beta 7.0.8