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

Aditya Gilra aditya_gilra at yahoo.com
Wed Nov 9 11:32:55 GMT 2011

Thanks Padraig,

I'm sticking to multiple neuroml files for now rather than the single file option.

However, there's a glitch in the multiple files option. When you export to neuroml as a single file, the temperature for the simulation is set as a meta:property (along with simulation time and dt). However, when exporting as multiple files, the Level3 file does not contain any meta:property tags for these. Could you include that?

I was quite surprised by the difference that 32 deg Celsius vs 35 deg Celsius makes to the action potential in the granulecell example model (KDR tau is temperature dependent) [Took me a while to figure out what was wrong!].


>From: P Gleeson <p.gleeson at ucl.ac.uk>
>To: Aditya Gilra <aditya_gilra at yahoo.com>
>Cc: "neuroconstruct at ucl.ac.uk" <neuroconstruct at ucl.ac.uk>; neuroml-technology at lists.sourceforge.net
>Sent: Wednesday, 9 November 2011 4:18 PM
>Subject: Re: [neuroConstruct] channel units bug in exporting a single neuroml file
>Hi Aditya,
>On 07/11/11 12:13, Aditya Gilra wrote: 
>>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
>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?)
>>Aditya Gilra.
neuroConstruct mailing list neuroConstruct at ucl.ac.uk http://www.mailinglists.ucl.ac.uk/mailman/listinfo/neuroconstruct Please note that the neuroConstruct mailing list is publicly archived
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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