These are chat archives for openworm/ChannelWorm

10th
Nov 2016
Neil Shah
@shah-n
Nov 10 2016 01:19
I received run time errors when running the python files which build the EGL-19 and SLO-2 ion channels.
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'
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'
Neil Shah
@shah-n
Nov 10 2016 01:31
The EGL-36 ion channel gets built, but the file is recognized as a text file instead of an XML file on Ubuntu.
Vahid Ghayoomie
@VahidGh
Nov 10 2016 08:04
@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!