These are chat archives for openworm/ChannelWorm

11th
Nov 2016
Stephen Larson
@slarson
Nov 11 2016 16:34
@VahidGh Any idea how @shah-n can fix the error?
Stephen Larson
@slarson
Nov 11 2016 17:36
@VahidGh — looks like EGL-19-2.py works where EGL-19.py doesn’t. Can we replace the one that doesn’t work?
Stephen Larson
@slarson
Nov 11 2016 17:48
@VahidGh — we are running into problems that there is no method called “ss_plots” in modelators.py -- this is being called in EGL-19-2.py and SLO-2.py -- do you know why there is no ss_plots? Maybe we are not importing something we need?
Vahid Ghayoomie
@VahidGh
Nov 11 2016 20:03
@slarson, Since there were some examples to show how to use cwFitter, I didn't go further to update all examples with new changes.
We were going to integrate the Django app with cwFitter, that I switched to the predictor project.
Stephen Larson
@slarson
Nov 11 2016 20:05
@VahidGh Gotcha. Well @shah-n is aiming to go through and read EGL-36.py to best understand what is doing, and to add comments to it. Then, he’ll read through EGL-19-2.py, comment it, and understand how they are similar / different. Your perspectives on what are the pros / cons of each will help. We’d like to help out meaningfully to be able to convert all ion channel data into neuroml files. Does this seem reasonable? How would you advise us to proceed?
Vahid Ghayoomie
@VahidGh
Nov 11 2016 20:07
Great, I suggest starting with a new channel based on EGL-36.
For example SHK-1, with ID=16.
Stephen Larson
@slarson
Nov 11 2016 20:11
Nice :thumbsup: I think that will be a great one once we can make sure that EGL-19-2.py SLO-2.py is also working again.
I also want to loop in @rgerkin here to say that in addition to this, we want to flesh out the SciUnit aspect of these that is exemplified in the iPython notebook he made here: https://github.com/openworm/ChannelWorm/blob/0b1c1f49b71785f5333e3c86d2ed97832d75a8f5/tests/SCU_IVCurve_Model.ipynb
That example could use some updating, since the latest fits from the fitter project are much better than what is shown in that notebook
Vahid Ghayoomie
@VahidGh
Nov 11 2016 20:37
@slarson, We can also start with some intros to the fitting process.
I would be glad to have a meeting with @shah-n to discuss more.
Stephen Larson
@slarson
Nov 11 2016 22:15
OK great @VahidGh — I’m sending you an invite for next Friday for getting together with Neil (anyone else welcome). Let me know if that time doesn’t work for you