A repository to integrate data, information, scripts, and models of ion channels in C. elegans
Here is the EGL-19 error:
Traceback (most recent call last):
File "EGL-19.py", line 66, in <module>
best_candidate = candidates.optimize(do_plot=True, seed=1234)
File "/home/computer/git/channelworm/src/neurotune/neurotune/optimizers.py", line 142, in optimize
individuals_file=ind_file)
File "/home/computer/.local/lib/python2.7/site-packages/inspyred/ec/ec.py", line 434, in evolve
initial_fit = evaluator(candidates=initial_cs, args=self._kwargs)
File "../../../channelworm/fitter/evaluators.py", line 141, in evaluate
self.mySimulator = Simulator(self.sim_params,cand_var,cell_var,self.bio_params['gate_params']).patch_clamp()
File "../../../channelworm/fitter/simulators.py", line 22, in init
self.pc_type = sim_params['pc_type']
KeyError: 'pc_type'
Traceback (most recent call last):
File "EGL-19.py", line 66, in <module>
best_candidate = candidates.optimize(do_plot=True, seed=1234)
File "/home/computer/git/channelworm/src/neurotune/neurotune/optimizers.py", line 142, in optimize
individuals_file=ind_file)
File "/home/computer/.local/lib/python2.7/site-packages/inspyred/ec/ec.py", line 434, in evolve
initial_fit = evaluator(candidates=initial_cs, args=self._kwargs)
File "../../../channelworm/fitter/evaluators.py", line 141, in evaluate
self.mySimulator = Simulator(self.sim_params,cand_var,cell_var,self.bio_params['gate_params']).patch_clamp()
File "../../../channelworm/fitter/simulators.py", line 22, in init
self.pc_type = sim_params['pc_type']
KeyError: 'pc_type'
The optimization for SLO-2 runs successfully, but the following run-time error gets produced.
Traceback (most recent call last):
File "SLO-2.py", line 222, in <module>
myModelator.compare_plots(sampleData,bestSim,show=True)
File "../../../channelworm/fitter/modelators.py", line 192, in compare_plots
x_var = sampleData['VClamp']['x_var']
KeyError: 'x_var'
File "SLO-2.py", line 222, in <module>
myModelator.compare_plots(sampleData,bestSim,show=True)
File "../../../channelworm/fitter/modelators.py", line 192, in compare_plots
x_var = sampleData['VClamp']['x_var']
KeyError: 'x_var'
@shah-n, Thanks for checking this. The example file generating EGL-36 model, is using the latest version of cwFitter that getting inputs from DB instead of files (compare the initiators of EGL-36 and SLO-2).
Other examples should be updated as well based on these changes.
We have a plan to complete data and build models for ion channels with digitized data from patch-clamp experiments.
Feel free to play with scripts and models and let me know if there is any question!
Other examples should be updated as well based on these changes.
We have a plan to complete data and build models for ion channels with digitized data from patch-clamp experiments.
Feel free to play with scripts and models and let me know if there is any question!
We were going to integrate the Django app with cwFitter, that I switched to the predictor project.
@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?
For example SHK-1, with ID=16.
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
If you give us a few minutes; we are pushing out what neil has done to github
then we will send you a link and you can comment on it and we can discuss
@shah-n, I haven't tested it on Windows yet. If the error occurs when importing files from relative paths, then it could be due to fore-slash/back-slash issue in paths. We should consider using
However, if the error occurs when trying to import installed packages, maybe using Virtualenv, Ananconda, etc... could help!
Thanks for mentioning this issue.
os.path.join() instead of fore-slash directory separators.However, if the error occurs when trying to import installed packages, maybe using Virtualenv, Ananconda, etc... could help!
Thanks for mentioning this issue.
@shah-n, Have you changed the optimization method (
By default it's value is
Also, make sure to change parameters like file_name, etc. for generating a new .nml file.
opt parameter)?By default it's value is
None, so the optimized values would be those hard-coded ones. If you choose one of the available options like -pso, then you will notice that it takes some time for fitter to optimize the curves with new values and generate new plots.Also, make sure to change parameters like file_name, etc. for generating a new .nml file.
The digitizer app has also a feature to export data to csv files after digitization. So, if you need to work independent of this DB you can use this method.
@VahidGh: Do these comments agree with your understanding of EGL-36.py? https://github.com/openworm/ChannelWorm/compare/master...shah-n:master
Good Day! Just a concept of an experiment 3D (worm scheme2D vs time1D) chart. Sorry if something like this already exists. Wonder if something like this can be added to experiment output diagrams. And also which functionalities can be added to this. Currently it does slices and tries to find possible cascades from neuron https://github.com/Brain302/somebrowser/blob/master/README.md