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openworm / OpenWorm

Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
http://openworm.org
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Remove Glutamate_GJ etc in neuroConstruct project #50

Closed pgleeson closed 10 years ago

pgleeson commented 11 years ago

These names have been given to the "neurotransmitter" in the XL spreadsheet for gap junctions, e.g.

AIAL ASIL GapJunction 2 Acetylcholine_GJ

However, this only means: There are 2 gap junction connections between AIAL and ASIL (and AIAL's chemical synapses' neurotransmitter is Acetylcholine)

Thankfully there is an equivalent entry for the other direction too:

ASIL AIAL GapJunction 2 Glutamate_GJ

These should only be added as one gap junction connection in the nC project between AIAL and ASIL with 2 connections.

As a first approximation all GJ connections can have the same strength, set by a new Cell Mechanism GapJunction (as opposed to each connection having a cell mechanism Acetylcholine_GJ etc.)

pgleeson commented 11 years ago

Closed with 51c8bec6a2298ac2a2490b495ad5da7966a3063c

pgleeson commented 11 years ago

Check GABA_GJ in project

gidili commented 11 years ago

@pgleeson I remember you were talking about cleaning up the neuroConstruct proj - Is this issue something that was addressed while in Paris?

rayner commented 10 years ago

Hi, I'm having a look at this, and it looks like there was a "Generic_GJ" cell mechanism created for this purpose, but the connections in the neuroConstruct project never got changed to use it. Is this still the way we want to proceed?

If so, it looks like I can update all of the gap junction connections in CElegansNeuronTables.xls to have "Generic_GJ" in the "neurotransmitter" column, then run UpdateSynapses.py to re-import all of the data from the spreadsheet into the neuroConstruct project. We could then delete all the other superfluous "whatever_GJ" cell mechanisms.

pgleeson commented 10 years ago

Thanks for pointing this out @rayner. These should indeed be updated in the CElegansNeuronTables.xls, but there are a few other small inconsistencies between the spreadsheet & nC that I just want to iron out & I have to update some of the other scripts too, e.g. RegenerateConnectome.py. Will test what I have & try to commit this tomorrow...

pgleeson commented 10 years ago

I've updated the nC project and the spreadsheet with these fixes. See https://github.com/openworm/CElegansNeuroML/commit/99eb18f9074d1b79aa14eb9b6f1fc074b7e858cd