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OpenSourceBrain / PurkinjeCell

GitHub repository for an OSB project containing a cerebellar Purkinje cell based on De Schutter & Bower 1994
http://www.opensourcebrain.org/projects/purkinjecell
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NeuroML v2 versions of channels? #2

Open JustasB opened 7 years ago

JustasB commented 7 years ago

Are there NML v2 versions of the channels somewhere? I could not find them in this project, and the converter resulted in files with "Not yet implemented" message. Are there any plans to support such conversion somewhere?

Details below: generatedNeuroML2 folder only has the leak channel.

Using the ChannelMLConvert converter on e.g. this .xml channel file (or other channel files), results in an .nml file with "Not implemented yet" instead of gating dynamics.

It seems that the converter has problems with the current_voltage_relation construct seen on this line.

CC: @scrook

JustasB commented 7 years ago

@pgleeson Can you let us know if there are NMLv2 versions of the channels available for this model? Or if there are any ongoing v1->v2 conversion plans, or updates to the v1->v2 converter?

CC: @scrook

pgleeson commented 7 years ago

@JustasB Sorry I missed this the first time round. There is not a NMLv2 version of this model since the NeuroMLv1 version was never fully validated as matching the original GENESIS code. And even then, there is an issue about the stability/correctness of the GENESIS model which had been converted to Neuron and highlighted some issues: https://github.com/OpenSourceBrain/PurkinjeCell/issues/1.

So this project basically needs someone to spend time going through the original paper and code, and understanding the issues and converting what's useful to convert. I've asked a few students over the years and no joy yet...

A more likely scenario is to find someone to convert a more recent Purkinje cell model, e.g. https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=229585, but that's not started yet.

So in short, I wouldn't reuse any components of this model in NML2 in NeuroML-DB. As mentioned to @scrook, the single star for NeuroML2 support here: http://www.opensourcebrain.org/projects/purkinjecell should be a red flag. Please do ask though if it does look like a project/model is there in valid NML2.