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Hi Derek,<br>
<br>
Replying on the neuroConstruct mailing list. If there are any other
questions which may be of general interest to users, send them to this
address and I'll try to handle them.<br>
<br>
MorphML files can be imported into neuroConstruct via the tab Cell
Types. Select Add new cell type to project, and in the drop down box
select NeuroMLConverter. Specify where the file is and press Create. It
might be best to import first into a new project (containing the
example cells, channels, etc.) to test. <br>
<br>
The imported cell will probably be invalid if there are no channels
specified (i.e. if it's not Level 2). Viewing the cell and placing the
LeakConductance on all sections is a good start towards a valid cell in
this case (default values of membrane leak conductance, capacitance,
axial resistance will have to be updated though). Even if the MorphML
file is Level 2 (strictly then a NeuroML file aot MorphML) and channels
are present, these might not necessarily be in the project (e.g. if the
cell has been exported from NEURON with the files at:
<a class="moz-txt-link-freetext"
href="http://neuroml.svn.sourceforge.net/viewvc/neuroml/nrn2NeuroML/">http://neuroml.svn.sourceforge.net/viewvc/neuroml/nrn2NeuroML/</a>).
These
channel names can be made match the cell mechanism names used in the nC
project by a find & replace on the XML file before import, though
I'm working to automate this when the file is imported.<br>
<br>
MorphML/NeuroML files from any source can be imported (as long as they
are valid at <a class="moz-txt-link-freetext"
href="http://www.morphml.org:8080/NeuroMLValidator">http://www.morphml.org:8080/NeuroMLValidator</a>),
so if there
is any problem with import of a self generated, valid file, please let
me know. Also, manually editing of a MorphML file and reimporting it
might be the best way to edit cells if there is a specific function not
implemented through the neuroConstruct GUI (e.g. bulk renaming of
sections/groups).<br>
<br>
Hope this helps,<br>
Padraig<br>
<br>
<br>
<br>
<br>
<br>
<br>
-------- Original Message --------
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<tr>
<th align="right" nowrap="nowrap" valign="baseline">Subject: </th>
<td>neuroConstruct User Group</td>
</tr>
<tr>
<th align="right" nowrap="nowrap" valign="baseline">Date: </th>
<td>Thu, 6 Sep 2007 10:05:57 -0500</td>
</tr>
<tr>
<th align="right" nowrap="nowrap" valign="baseline">From: </th>
<td>Derek James <a class="moz-txt-link-rfc2396E"
href="mailto:djames@gmail.com"><djames@gmail.com></a></td>
</tr>
<tr>
<th align="right" nowrap="nowrap" valign="baseline">To: </th>
<td><a class="moz-txt-link-abbreviated"
href="mailto:p.gleeson@ucl.ac.uk">p.gleeson@ucl.ac.uk</a></td>
</tr>
</tbody>
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<br>
<br>
...<br>
<br>
I'm interested in modeling the neocortex, at a fairly coarse-grained
level, and I'm planning on generating XML files to be imported into
neuroConstruct for visualization. The tutorial simply says "morphML
files may be imported into neuroConstruct", but isn't very specific
about how this is done. <br>
<br>
...<br>
<br>
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