<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Thanks Padraig,</span></div><div><span><br></span></div><div><span>I'm sticking to multiple neuroml files for now rather than the single file option.<br></span></div><div><span>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.</span> Could you include that?</div>
<div><br><span></span></div><div><span>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!].<br></span></div><div><br></div><div>Best,</div><div>Aditya.<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><font face="Arial" size="2"><hr size="1"><b><span style="font-weight:bold;">From:</span></b> P Gleeson <p.gleeson@ucl.ac.uk><br><b><span style="font-weight: bold;">To:</span></b> Aditya Gilra <aditya_gilra@yahoo.com><br><b><span style="font-weight: bold;">Cc:</span></b> "neuroconstruct@ucl.ac.uk" <neuroconstruct@ucl.ac.uk>;
neuroml-technology@lists.sourceforge.net<br><b><span style="font-weight: bold;">Sent:</span></b> Wednesday, 9 November 2011 4:18 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [neuroConstruct] channel units bug in exporting a single neuroml file<br></font><br><div id="yiv1353461167">
<div>
Hi Aditya,<br>
<br>
<br>
On 07/11/11 12:13, Aditya Gilra wrote:
<blockquote type="cite">
<div style="color:rgb(0, 0, 0);background-color:rgb(255, 255,
255);font-family:arial, helvetica, sans-serif;font-size:12pt;">
<div>Hi,</div>
<div>Do we have a web interface for bug reports or should I mail
to this list?<br>
</div>
</div>
</blockquote>
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.<br>
<blockquote type="cite">
<div style="color:rgb(0, 0, 0);background-color:rgb(255, 255,
255);font-family:arial, helvetica, sans-serif;font-size:12pt;">
<div>Am using neuroconstruct 1.5.1.</div>
<div>I exported a single/unified neuroml file for say the
granulecell in the example models,</div>
<div>i.e. export->neuroml-> select 'level 3' and tick
'generate single neuroml level 3 file' and then click
'generate all neuroml scripts'.</div>
<div>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.</div>
</div>
</blockquote>
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. <br>
<br>
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"...<br>
<br>
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.<br>
<br>
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. <br>
<br>
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.<br>
<br>
Regards,<br>
Padraig<br>
<br>
<br>
<blockquote type="cite">
<div style="color:rgb(0, 0, 0);background-color:rgb(255, 255,
255);font-family:arial, helvetica, sans-serif;font-size:12pt;">
<div>Let me know when you fix this (after you've verified this
is a bug.) (I suppose Padraig will be following up?)<br>
</div>
</div>
</blockquote>
<blockquote type="cite">
<div style="color:rgb(0, 0, 0);background-color:rgb(255, 255,
255);font-family:arial, helvetica, sans-serif;font-size:12pt;">
<div>Thanks,</div>
<div>Aditya Gilra.</div>
<div><br>
</div>
</div>
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</blockquote>
<br>
<br>
<pre class="yiv1353461167moz-signature">--
-----------------------------------------------------
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
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