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  • Aug 03 10:31
    topazand starred openworm/ChannelWorm
  • Mar 31 2019 13:39
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Vahid Ghayoomie
@VahidGh
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
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
Vahid Ghayoomie
@VahidGh
That would be great
An interesting part is that they've provided a REST API for accessing raw data
Richard C Gerkin
@rgerkin
@VahidGh You mean the ion channel site you just linked?
Vahid Ghayoomie
@VahidGh
yep
This way we can estimate each channel model by the predictor I'm working on, then using those APIs, find the most similar model for the ion channel of interest, and then convert it to NeuroML
Vahid Ghayoomie
@VahidGh
A problem with ion channel kinetics (especially gating) is that there could be two channels from the same family and subfamily but with different kinetics in different species
And vice versa for channels with different families but the same kinetics
So, we can not just rely on families
By combining two approaches, we can estimate gating kinetics from the protein and structural properties, and then find the other parameters (such as activation/inactivation and their powers) from similarity/family based approaches, and then having the best estimated model
Stephen Larson
@slarson
Cool idea
Richard C Gerkin
@rgerkin
Yes, I like it
@VahidGh How would you search by model similarity? Does the API let you do that?
Vahid Ghayoomie
@VahidGh
@rgerkin, using the browser we can limit the models we are interested in, and then using the APIs getting the raw data for each plot, and then by comparing with our estimations, we can find the best match
I also am waiting for their publication to see what are the features for the kinetics similarity , etc
We can also use the same approach for the second part of our approach
Richard C Gerkin
@rgerkin
Oh so you are selecting models based on similarity to your models' output plots, or to your digitized data plots, or to model parameter similarity?
@VahidGh
Vahid Ghayoomie
@VahidGh
This is what they intend to do, and the aim of the project
Richard C Gerkin
@rgerkin
@VahidGh I mean what methods are you taking:
1) Select based on similarity to your model's simulation plots
or 2) Select based on similarity to data plots of interest
or 3) Select based on similarity of model parameters to your fitted model's parameters
Vahid Ghayoomie
@VahidGh
Yeah, the first one -- I'm estimating the kinetics, then generating some putative model, and then comparing mine with the most similar one within the same family to complete my model based on what there have been generated for the same family
Richard C Gerkin
@rgerkin
Cool
Vahid Ghayoomie
@VahidGh
They don't work with the parameters, they just store traces, and the similarity is based on traces
They've also normalized currents, so there is no problem with max conductance
We just need to include the models within the cells, and then optimize parameters like conductance with some approach taken by @pgleeson in C302
summerworm
@sumwor
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
@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
@VahidGh thanks! But why there is nothing but None in the website?
Padraig Gleeson
@pgleeson
@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
@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
@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
@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.
Eric T Cormack
@theodinspire
Hello! I'm trying to install ChannelWorm and at least get it running, but I keep hitting my head against the well
wall*