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Hi Aditya,<br>
<br>
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.<br>
<br>
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...).<br>
<br>
Cheers,<br>
Padraig<br>
<br>
<br>
<br>
On 09/11/11 11:32, Aditya Gilra wrote:
<blockquote
cite="mid:1320838375.90782.YahooMailNeo@web95901.mail.in.yahoo.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); 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 <a class="moz-txt-link-rfc2396E" href="mailto:p.gleeson@ucl.ac.uk"><p.gleeson@ucl.ac.uk></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Aditya Gilra <a class="moz-txt-link-rfc2396E" href="mailto:aditya_gilra@yahoo.com"><aditya_gilra@yahoo.com></a><br>
<b><span style="font-weight: bold;">Cc:</span></b>
<a class="moz-txt-link-rfc2396E" href="mailto:neuroconstruct@ucl.ac.uk">"neuroconstruct@ucl.ac.uk"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:neuroconstruct@ucl.ac.uk"><neuroconstruct@ucl.ac.uk></a>;
<a class="moz-txt-link-abbreviated" href="mailto:neuroml-technology@lists.sourceforge.net">neuroml-technology@lists.sourceforge.net</a><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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<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
<a moz-do-not-send="true" rel="nofollow" class="yiv1353461167moz-txt-link-abbreviated" ymailto="mailto:p.gleeson@ucl.ac.uk" target="_blank" href="mailto:p.gleeson@ucl.ac.uk">p.gleeson@ucl.ac.uk</a>
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<pre class="moz-signature" cols="72">--
-----------------------------------------------------
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
<a class="moz-txt-link-abbreviated" href="mailto:p.gleeson@ucl.ac.uk">p.gleeson@ucl.ac.uk</a>
-----------------------------------------------------</pre>
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