There should be a few well curated OSB projects whose repositories contain a reasonably complete set of NMLv1 files for a cell or network model, for testing purposes.
Note most neuroConstruct projects in OSB have nC based morphology files & ChannelML etc. in certain nC specific folder structure, but don't contain a single complete set of NML1 files, as is the case for many NeuroML 2 models.
As requested by @scrook
Some options for these are:
(boxes will be ticked as they are added)
Adding generated NeuroML v1 files
Related to OpenSourceBrain/redmine#119
The ApicalSyn and MultiDecaySyn files aren't there for the Vervaeke et al. Golgi Cell Network
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?
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.
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.
Arizona State University
From: Padraig Gleeson [firstname.lastname@example.org]
Sent: Sunday, July 27, 2014 10:10 AM
Cc: Sharon Crook
Subject: Re: [redmine] Make a core set of projects with NeuroML v1.8.1 generated files (#119)
Reply to this email directly or view it on GitHubhttps://github.com/OpenSourceBrain/redmine/issues/119#issuecomment-50279325.
@pgleeson is this card done? Can we close it?
@adrianq, let's leave this open for now, I'll look again at this when I try out mapping the Traub model to NMLv2...
@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
@scrook Synapses added in nml1 format with OpenSourceBrain/Thalamocortical@0618ca1
Thanks @pgleeson! What are the plans for update to v2?
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?
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.