Public channel for all NeuroML related discussion. Documentation at https://docs.neuroml.org
pgleeson on v0.7.1
pgleeson on development
update np json To v0.7.1 Merge pull request #175 from Ne… (compare)
github-actions[bot] on gh-pages
Update documentation (compare)
sanjayankur31 on master
Add fig for file organisation Merge pull request #132 from Ne… (compare)
pgleeson on pg_updates
Add fig for file organisation (compare)
pgleeson on pg_updates
Merge pull request #130 from Ne… typo fix: rick -> rich Merge pull request #131 from ra… (compare)
pynml.run_lems_with_jneuroml_neuron
function call to skip compilation of mod files by adding the compile_mods=false
argument to it. So it should use the files you just compiled and run correctly 🤞
libnrnmech.dylib
to check for successful compilation
x86_64
directory with the compiled library.
git clean -dfx
will do it for you
nrngui exampl1.hoc
then in /NeuroML2 python export_nml2.py
nrn_load_dll("./channels/arm_64/.libs/libnrnmech.so")
it was supposed to be 'x86_64'.
libnrnmech.so
in the given "arm_64" dir.
nrnivmodl
in the folder with the mod files, make sure the x86_64
folder is there and then run pynml-modchananalysis kfast -stepV 5 -temperature 37 -modFile kfast.mod
. Worked fine for me.
I don't think we've advertised HARMONY 2022 here folks! Please register, it's free:
A reminder about the NeuroML Development Workshop later today!
Time: 15:00-18:00 UTC. Scheduled for 3 hours, but everyone's busy, so let's try to get through the agenda in 2 hours, and leave the rest for open discussion.
Zoom link: https://ucl.zoom.us/j/91720715131?pwd=YmtLa29jd0ROWnNMVGovVzhCd0NIdz09 (please register for Harmony too!)
Agenda: https://docs.google.com/document/d/1GOkmylIlLH3dbxB2Pmis7VxFPzipstLBdXn5uBu4rv8/edit
I'm trying to write some NeuroML to capture arbitrary kinetics that I can then convert via pynml into a MOD file for simulation, and I'm getting close to understanding how to do it, but I'm not quite there... what I have is: https://www.dropbox.com/s/c1oqm6dvsd8u1ex/test6.nml?dl=0
Questions:
pynml-modchananalysis
and pynml-channelanalysis
. Help me locate them.
Hi! I am currently trying to convert the all-active cell model 497233223 of this electrophysiology.
The cell contains information about e_pas and g_pas which are the leakage reverse potential and specific leakage conductance of the pas channel respectively.
When converting this to NeuroML, the e_pas value is set using the erev parameter (see here).
How to translate g_pas to NeuroML? @pgleeson @sanjayankur31