Make a core set of projects with NeuroML v1.8.1 generated files #119

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pgleeson opened this Issue Jul 15, 2014 · 12 comments

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@pgleeson
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@pgleeson pgleeson self-assigned this Jul 15, 2014
@pgleeson pgleeson added a commit to OpenSourceBrain/GranuleCell that referenced this issue Jul 17, 2014
@pgleeson pgleeson Adding generated NeuroML v1 files b8c8810
@scrook
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scrook commented Jul 22, 2014

The ApicalSyn and MultiDecaySyn files aren't there for the Vervaeke et al. Golgi Cell Network

@scrook
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scrook commented Jul 26, 2014

Looking at the cells for the Traub model, there are a large number of synapses that start with "syn_" that aren't here. There are about 10 synapses present but these are not?

@pgleeson
Member

True... unfortunately there are about 140 different synapses in that model for each of the different pre/post/type combinations, e.g. Syn_NMDA_FRBPyr_SupFS... They're not even in the nC project but generated after download as described here: http://www.opensourcebrain.org/projects/thalamocortical/wiki

Would you like all these added? Will make the repo a bit bigger, but Github should manage it fine.

@scrook
Member
scrook commented Jul 27, 2014

Yeah, I'm not sure. The full model has 14 cells and thus needs all of these synapses but the
reduced model here has only 5 cells I think so it's not clear how many of the synapses are really
necessary for that version. Maybe we can chat a bit about the different versions of the model
and I can figure out what we should include in this network in the database.

Thanks!
sc

Sharon Crook
Arizona State University
http://math.la.asu.edu/~crook
http://neuroml.org


From: Padraig Gleeson [notifications@github.com]
Sent: Sunday, July 27, 2014 10:10 AM
To: OpenSourceBrain/redmine
Cc: Sharon Crook
Subject: Re: [redmine] Make a core set of projects with NeuroML v1.8.1 generated files (#119)

True... unfortunately there are about 140 different synapses in that model for each of the different pre/post/type combinations, e.g. Syn_NMDA_FRBPyr_SupFS... They're not even in the nC project but generated after download as described here: http://www.opensourcebrain.org/projects/thalamocortical/wiki

Would you like all these added? Will make the repo a bit bigger, but Github should manage it fine.


Reply to this email directly or view it on GitHubhttps://github.com/OpenSourceBrain/redmine/issues/119#issuecomment-50279325.

@adrianq adrianq added the in progress label Jul 28, 2015
@adrianq
adrianq commented Aug 4, 2015

@pgleeson is this card done? Can we close it?

@pgleeson
Member

@adrianq, let's leave this open for now, I'll look again at this when I try out mapping the Traub model to NMLv2...

@pgleeson
Member

@adrianq I think this is as much as we can do for now with NMLv1 files, so I'll close this. There are unlikely to be many new OSB projects in pure v1.8.1.

@scrook you were asking about the missing synapse files for Thalamocortical. I've added an issue here: OpenSourceBrain/Thalamocortical#2 for this and will look into it when updating the Traub model for v2

@pgleeson pgleeson closed this Sep 24, 2015
@pgleeson pgleeson removed the in progress label Sep 24, 2015
@pgleeson
Member
pgleeson commented Jun 1, 2016

@scrook Synapses added in nml1 format with OpenSourceBrain/Thalamocortical@0618ca1

@scrook
Member
scrook commented Jun 1, 2016

Thanks @pgleeson! What are the plans for update to v2?

@pgleeson
Member
pgleeson commented Jun 2, 2016

We're working on updating/curating those at the moment. @RokasSt is working on the model as part of the Google Summer of Code.

Is there any specific metadata you'd like included/updated in the files?

@scrook
Member
scrook commented Jun 7, 2016

The main metadata that we are using is the publication including authors and pubmed id, an appropriate NeuroLex id (or similar ontological reference), and any keywords from the paper or that we add. Also other references such as ModelDB ID and/or OSB.

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