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Make a GO-CAM mega-model #1265

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kimrutherford opened this issue Mar 3, 2025 · 5 comments
Open

Make a GO-CAM mega-model #1265

kimrutherford opened this issue Mar 3, 2025 · 5 comments
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@kimrutherford

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@kimrutherford
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Combine all the GO-CAMs into a single Cytoscape view.
@kimrutherford kimrutherford self-assigned this Mar 3, 2025
kimrutherford added a commit to pombase/pombase-gocam-process that referenced this issue Mar 4, 2025
@kimrutherford
Remove bon crate - not used for now
19c5ca8 
Refs pombase/pombase-chado#1265
kimrutherford added a commit to pombase/pombase-gocam-process that referenced this issue Mar 4, 2025
@kimrutherford
Remove unneeded fields from GoCamModel
0daf78c 
Add node_iterator()

Refs pombase/pombase-chado#1265
kimrutherford added a commit to pombase/pombase-chado-json that referenced this issue Mar 4, 2025
@kimrutherford
Update pombase-gocam-process version, fix warning
dcfa9f4 
Refs pombase/pombase-chado#1265
kimrutherford added a commit to pombase/pombase-gocam-process that referenced this issue Mar 4, 2025
@kimrutherford
Make GoCamModel serializable and deserializable
0f75311 
Refs pombase/pombase-chado#1265
kimrutherford added a commit to pombase/pombase-gocam-process that referenced this issue Mar 4, 2025
@kimrutherford
Add a very basic test for loading a GoCamModel
2fea269 
Refs pombase/pombase-chado#1265
kimrutherford added a commit to pombase/pombase-gocam that referenced this issue Mar 4, 2025
@kimrutherford
Add GoCamModel from pombase-gocam-process
8146117 
Refs pombase/pombase-chado#1265
kimrutherford added a commit to pombase/pombase-gocam that referenced this issue Mar 4, 2025
@kimrutherford
Change Individual functions to methods
0c372cd 
Refs pombase/pombase-chado#1265
kimrutherford added a commit to pombase/pombase-gocam that referenced this issue Mar 4, 2025
@kimrutherford
Make Individual methods public
99f3e22 
Refs pombase/pombase-chado#1265
kimrutherford added a commit to pombase/pombase-gocam-process that referenced this issue Mar 4, 2025
@kimrutherford
Update pombase-gocam dependency
fa50326 
Move code to pombase-gocam.

Refs pombase/pombase-chado#1265
@kimrutherford
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So we have a way to view the (eventual) mega-model, I've integrated the code for my dodgy GO-CAM viewer into the main website, although it's not linked from anywhere.
To view a GO-CAM, use a URL like this and edit the GO-CAM ID:
https://www.pombase.org/gocam_view/full/66187e4700003150

kimrutherford added a commit to pombase/pombase-chado-json that referenced this issue Mar 4, 2025
@kimrutherford
Update pombase-gocam dependencies
9f92435 
Refs pombase/pombase-chado#1265
kimrutherford added a commit to pombase/pombase-gocam that referenced this issue Mar 4, 2025
@kimrutherford
Add merge_models() function
f7ac75b 
Doesn't yet merge identical nodes.

Refs pombase/pombase-chado#1265
@kimrutherford
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Here's how it looks with all the models in one Cytoscape, without joining them together:
https://desktop.kmr.nz/local/cy_test.html

Unfortunately it doesn't work very well at all. Let chat Zoom.

@ValWood
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ValWood commented Mar 4, 2025

So how do I see the mega model, or isn't that available yet?

@ValWood
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ValWood commented Mar 4, 2025

I just saw you comment, looking

@ValWood
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ValWood commented Mar 4, 2025

It beautiful !

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