[neuroConstruct] channel units bug in exporting a single neuroml
file
P Gleeson
p.gleeson at ucl.ac.uk
Thu Nov 10 18:01:38 GMT 2011
Hi Aditya,
That's fixed in the neuroConstruct SVN now. The meta:property tags are
of course highly non standard. The dt and sim duration belong rightly in
a SED-ML file, along with details of what to save, plot etc. I'm working
on an option exporting valid SED-ML beside the NeuroML.
With regards to the temperature, this could be set in the SED-ML too,
though there will probably have to be some concept of a (global)
temperature in a NeuroML 2 file (e.g. as a property of a <network>, or
maybe <population>, as different cells in different parts of the brain
could in theory have different temps...).
Cheers,
Padraig
On 09/11/11 11:32, Aditya Gilra wrote:
> 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!].
>
> Best,
> Aditya.
>
> ------------------------------------------------------------------------
> *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:
>> 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.
>
> Regards,
> Padraig
>
>
>> 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 <mailto:p.gleeson at ucl.ac.uk>
> -----------------------------------------------------
>
>
>
--
-----------------------------------------------------
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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