These are chat archives for openworm/ChannelWorm

29th
Sep 2015
summerworm
@sumwor
Sep 29 2015 05:30
hey guys! I have a little question about the web app of Channelworm
in the ion channel form, the channel type column, every channel is None; None, So what exactly are we supposed to fill in that blank?
is it voltage-gated? ligand gated? or other kind of category? Or we just fill the blank with None; None no matter what?
Hope you can understand what I mean :) thanks!
Vahid Ghayoomie
@VahidGh
Sep 29 2015 07:12
@sumwor, good question -- The first one is usually the family (e.g. Voltage-gated Calcium channel, or CaV for EGL-19), but for the second one we can use for example one of these for EGL-19: L-type, HVA, high threshold
summerworm
@sumwor
Sep 29 2015 15:12
@VahidGh thanks! But why there is nothing but None in the website?
Padraig Gleeson
@pgleeson
Sep 29 2015 15:43
@VahidGh: "is there any script to convert a NEURON model to the NeuroML file". In short, no. Best option is pynml-channelanalysis/pynml-modchananalysis, as outlined here: http://www.opensourcebrain.org/docs#Converting_To_NeuroML2
Vahid Ghayoomie
@VahidGh
Sep 29 2015 16:24
@sumwor, This field was not clear for many of the channels and needed some manual curation. I decided to do this, one-by-one when getting deep into each channel.
@pgleeson, thanks
summerworm
@sumwor
Sep 29 2015 17:07
@VahidGh thanks a lot! And BTW, I found this C. elegans genome database which contains the channel protein data, is anyone ever heard of this? http://www.wormbook.org/chapters/www_neuronalgenome/neuronalgenome.html I think that could be really helpful :)
Vahid Ghayoomie
@VahidGh
Sep 29 2015 18:30
@sumwor, cool! I remember had a look at something like this long time ago, and used some texts and photos for our docs. Thanks for reminding this again. It's really helpful.