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