[neuroConstruct] channel units bug in exporting a single neuroml file

P Gleeson p.gleeson at ucl.ac.uk
Wed Nov 9 10:48:55 GMT 2011

Hi Aditya,

On 07/11/11 12:13, Aditya Gilra wrote:
> Hi,
> Do we have a web interface for bug reports or should I mail to this list?
Posting to the list is probably best, no forum or bug tracker for 
neuroConstruct at the moment... I've cc'd the NeuroML list too.
> Am using neuroconstruct 1.5.1.
> I exported a single/unified neuroml file for say the granulecell in 
> the example models,
> i.e. export->neuroml-> select 'level 3' and tick 'generate single 
> neuroml level 3 file' and then click 'generate all neuroml scripts'.
> Now this creates an nml file with <channels units="SI Units"> tag 
> amongst other tags. However, some of the channels continue to have 
> physiological units. There is no overriding units attribute in their 
> <channel_type> tags either. An example is the Gran_KA_98 channel. Of 
> course this problem does not occur if multiple xml files for each 
> channel, cell, network are created, since each channel has its own units.
Yes, it was a problem in the neuroConstruct single L3 file export... I 
had code in place to check for a mixture of SI & Physiological units in 
the ChannelML files but for some reason I took it out.

The option of adding a flag to the <channel_type> element to specify the 
units might be the simplest, but I really don't want to go updating the 
v1.x specs at this stage with so much going on for v2.0. If others feel 
strongly about it though let me know... This issue won't be a problem in 
v2, since all quantities must specify their own units (dimensions will 
be restricted in the component class definition), e.g. v="-60mV"...

While it would be possible in theory to make a general conversion 
utility (in Python or XSL) to change an SI v1.8.1 file into 
Physiological & vice versa, it would need to know what each quantity 
was, there would be no way to automate the conversion. Unfortunately not 
something I can spend time on with lots to do for v2.0.

So I'll put back in the check in nC if a user tries to export to a 
single L3 file containing a mix of SI & Physiol ChannelML files (and a 
warning when you press "Validate" that there is a mixture...). For such 
projects, the options would be to export as individual NeuroML files 
with one model component in each, or manually convert the ChannelML 
files to the same units. This latter option is painful I know, but I've 
just done this conversion for all the standard nC example projects.

Updating the latest neuroConstruct code and example projects with 
nCupdate.sh/nCupdate.bat will get you the fix and should be able to 
export them all to valid single Level 3 files.


> Let me know when you fix this (after you've verified this is a bug.) 
> (I suppose Padraig will be following up?)
> Thanks,
> Aditya Gilra.
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Padraig Gleeson
Room 321, Anatomy Building
Department of Neuroscience, Physiology&  Pharmacology
University College London
Gower Street
London WC1E 6BT
United Kingdom

+44 207 679 3214
p.gleeson at ucl.ac.uk

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