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  • Aug 03 10:31
    topazand starred openworm/ChannelWorm
  • Mar 31 2019 13:39
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Vahid Ghayoomie
@VahidGh
We can start with a simple model and then adding the other parameters
Stephen Larson
@slarson
@VahidGh is it possible yet to populate the ion channel models screen? https://channelwormdjango-channelworm.rhcloud.com/ion_channel/ion_channel_model
Vahid Ghayoomie
@VahidGh
It's possible using command lines, but still it's not been integrated with the UI
The server is not powerful enough to handle optimization tasks
Stephen Larson
@slarson
Gotcha. Have you been storing optimized models somewhere in the repo via command lines yet? I'm again, not as familiar about where they live
Richard C Gerkin
@rgerkin
This looks like a place where integration with NeuroML-DB could be useful
We want to store a bunch of ion channel models, provenance, etc. there, too
Vahid Ghayoomie
@VahidGh
@slarson, there are some examples here I was working on
@rgerkin, yeah
Stephen Larson
@slarson
@VahidGh Ok Cooooool!!
@VahidGh So you haven't had to go through NeuroML channels yet to do that optimization, yeah?
Because yeah, @rgerkin -- that could be interesting to add a step to convert to NeuroML channels & combine with NeuroML-DB. I'm not as familiar as to where that project is right now
Richard C Gerkin
@rgerkin
What is channel format now?
Vahid Ghayoomie
@VahidGh
Actually I'm doing the optimization and then passing the parameters to NeuroML file generators through this
Stephen Larson
@slarson
OIC so that's a subsequent step within the fitter framework!
Thanks for filling me in & sorry for my ignorance!
I think I got confused because you aren't writing them out into the repo
So that would be an option to add, potentially, right?
even though, hmm, looks like you are intending to do something like that here: https://github.com/openworm/ChannelWorm/blob/master/channelworm/fitter/examples/SLO-2.py#L277
Richard C Gerkin
@rgerkin
@VahidGh Looking at that code, are you just extracting channel parameters reported in the papers and then building NeuroML files with those parameters?
Vahid Ghayoomie
@VahidGh
@slarson, exactly :D
@rgerkin, Nope, I'm extracting the parameters from those figures
Richard C Gerkin
@rgerkin
Oh, but are they directly determinable from the figures or is there a modeling step there?
Things would be much easier if all data was reported in tables (in addition to figures).
Vahid Ghayoomie
@VahidGh
I'm getting the digitized data, then starting the optimization and testing different parameters, then storing the best model within a nml file
Richard C Gerkin
@rgerkin
"Best" in reproducing the figures from which you extracted the parameters, or some other figures?
Vahid Ghayoomie
@VahidGh
Yeah, there are some TODOs that was supposed to be completed by some "helping hands" :D
Richard C Gerkin
@rgerkin
@slarson @VahidGh Alright, I'm going to dive into an SLO-2 channel figure, maybe by analogy to the EGL-19 one I already did, and try to write a testing notebook for it.
Vahid Ghayoomie
@VahidGh
I'm really busy with the other milestone, and had some great progress, but lacking some super computer for the tasks such as grid searches I'm doing for feature selection made the work a bit slow. Universities are getting open by this week in Iran, and I hope I could improve the speed by having some powerful computers in our lab
Stephen Larson
@slarson
@rgerkin ok awesome!
Vahid Ghayoomie
@VahidGh
I'm trying to find some relationship between biophysical and biochemical features (like these of ion channel proteins and their kinetics
So far I could reach an estimation of the kinetics with the MAE of about ~9 mV
And decreasing the error day by day by playing with those features
The Scikit learn is a cool package, and getting master on it :D
Richard C Gerkin
@rgerkin
@VahidGh Scikit-learn is pretty great!
Vahid Ghayoomie
@VahidGh
@rgerkin, @slarson, Oh I forgot to mention this great work, recently launched: http://icg.neurotheory.ox.ac.uk/
And thanks to Dr. Crook for the clue
I talked to the guys behind this
To see if we can include my idea
They have some similar idea based on clustering techniques
And their publication is under review
My plan is to find those parameters from protein sequences and then for each channel, find the most similar model, and then include my parameters into the channel model
Vahid Ghayoomie
@VahidGh
unfortunately they don't have models for C. elegans, but we can use my approach to find out the best model for the channels we don't have patch clamp data for
Stephen Larson
@slarson
@VahidGh Wow just been looking on that site
that seems extremely relevant!
Richard C Gerkin
@rgerkin
@VahidGh Oh wow, surprised I haven't seen that
Stephen Larson
@slarson
Me too!
Vahid Ghayoomie
@VahidGh
The first version launched just a month ago
@rgerkin, @pgleeson, is there any script to convert a NEURON model to the NeuroML file?
Richard C Gerkin
@rgerkin
@VahidGh I think NEURON (the program) has NeuroML export. I don't know how well it works. Padraig would have the best word on this