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NeuroML version 1.8.0
Hi,
Version 1.8.0 has been put on the NeuroML website
(http://www.neuroml.org). The main change is that all of the ion channel examples have been updated to the latest version of ChannelML, i.e. using the structure:
<current_voltage_relation cond_law="ohmic" ...>
<gate name="m" instances="3">
<closed_state id="m0"/>
<open_state id="m"/>
<transition name="alpha" .../>
...
<current_voltage_relation/>
as opposed to the older structure which separated the gating information into <hh_gate>, etc. The XSL mappings for NEURON and GENESIS have been updated to handle the new format, and there is also an initial version of a mapping to PSICS channels.
Full details of the v1.8.0 changes are here:
http://www.neuroml.org/NeuroMLValidator/ViewNeuroMLFile.jsp?localFile=NeuroMLFiles/Schemata/v1.8.0/RELEASE_NOTES&viewFormat=plaintext
Regards,
Padraig
2009-01-19 16:51:05 UTC by pgleeson
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NeuroML v1.7.3
Hi,
The latest version of NeuroML, v1.7.3 has been put on the website. The validator application has been updated to use the new www.neuroml.org layout/colour scheme. The previous location for the validator (www.morphml.org:8080/NeuroMLValidator/) has been redirected to the new server, so the preferred URL for the web application is now:
http://www.neuroml.org/NeuroMLValidator/
The latest release notes are here, but the main thing to point out is a number of files in a new format for ChannelML, e.g.:
http://www.neuroml.org/NeuroMLValidator/ViewNeuroMLFile.jsp?localFile=NeuroMLFiles/Examples/ChannelML/NaChannel_newFormat.xml
http://www.neuroml.org/NeuroMLValidator/ViewNeuroMLFile.jsp?localFile=NeuroMLFiles/Examples/ChannelML/KA_Chan_NewFormat.xml
These changes have been made to take into account some of Robert Cannon's comments. The main change is that channels are now described in terms of multiple open and closed states, between which there can be a number of transitions, either described by forward and reverse transitions ("alpha and beta"), or in terms of the time course and steady state descriptions ("tau and inf"). For "traditional" HH channels there will be a single open and a single closed state for each gating complex, with multiple instances of these allowed (e.g. 3 m and 1 h for Na).
The mappings to NEURON mod format and GENESIS have been updated to allow either the old or this new format, and there is an XSL file for assisting conversion of the old format to the new (Convert NeuroML to Updated format links on the validation results page).
Please let me know if you have any comments on the new format. It will be discussed, along with the other suggested changes for NeuroML version 2 (http://www.neuroml.org/NeuroMLValidator/ReqVersion2.jsp), at a workshop on Biophysical Single Cell Modelling at UCL in March of next year. Participants for this small workshop have already been invited, but if you feel strongly that you have something to contribute, please get in touch.
Regards,
Padraig
2008-12-08 10:00:50 UTC by pgleeson
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Version 1.7.1
Hi,
The latest version of NeuroML, v1.7.1, has been put on the website.
Full release notes are at http://www.morphml.org:8080/NeuroMLValidator/NeuroMLFiles/Schemata/v1.7.1/RELEASE_NOTES but the main points are:
- A number of elements have had their names changed to standardise naming across the levels (e.g. specificAxialResistance to spec_axial_resistance). Both forms are still valid but to old form will be disallowed in v2.0. These changes and others planned for v2.0 are listed at http://www.morphml.org:8080/NeuroMLValidator/ReqVersion2.jsp.
- A number of utility files, including those for importing & exporting NeuroML from NEURON are listed at: http://www.morphml.org:8080/NeuroMLValidator/ToolsEtc.jsp. There is also a command line utility there for converting ChannelML files to directly mod and compiling them (along the lines of nrnivmodl).
Regards,
Padraig
2008-05-29 13:09:46 UTC by pgleeson
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Version v1.6
Version 1.6 of the validation app has been put live. Full release notes are here <http://www.morphml.org:8080/NeuroMLValidator/ViewNeuroMLFile.jsp?localFile=NeuroMLFiles/Schemata/v1.6/RELEASE_NOTES&viewFormat=plaintext>. The main points:
- Added a <status> element in Metadata (used in channel_type, synapse_type, ion_concentration currently) which can be used to indicate stable/in_progress/known_issues status of files. Can be used to automatically detect unstable parts of complex models. Also allows/encourages authors to add their names when they specify a status; aimed at eliminating anonymous comments in files hinting at some possible bug.
- 3 examples at each level are highlighted on the main page as particularly useful to learn the structure of the specifications (suggestions for enhancements welcome).
- Enabled links from elements in (formatted) XML view of examples to HTML representation of XSDs (e.g. link from <meta:notes> in any NeuroML file to the definition in HTML view of Metadata.xsd)
- Added Nicolas's XSDtoRNG.xsl for RelaxNG view of Schemas from HTML view of the XSDs.
Comments welcome.
Padraig
2007-07-03 14:06:57 UTC by pgleeson
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NeuroML version 1.5
A new version of the NeuroML specs have been put live at:
http://morphml.org:8080/NeuroMLValidator
The Release notes link on the main page gives the changes since v1.4,
but to summarise:
- Different Q10 rate adjustments for different gates, as in
GateDepQ10.xml, are now allowed, and supported in the NEURON/GENESIS
mappings
- Specification of a basic I&F mechanism is possible, see
IntFireMechanism.xml. Based on the COBA based I & F model as used in
Brette et al (2006) (http://arxiv.org/abs/q-bio.NC/0611089). The NEURON
mapping is based on the script files from
http://senselab.med.yale.edu/SenseLab/ModelDB/ShowModel.asp?model=83319.
Note: there is no GENESIS mapping for this mechanism, as none was
created for the paper, but mapping to other simulators used in the study
should be possible.
- Electrical inputs to the network can be specified. Two types are
possible, current pulse based and random stimulation. These should be
further developed to allow easier specification of input protocols, a
series of pulses, time dependent input rate, etc.
Comments and suggestions very welcome.
Regards
Padraig
2007-03-13 10:29:32 UTC by pgleeson
