GitHub - roybens/SimulatingVariants

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 443 Commits
.ipynb_checkpoints		.ipynb_checkpoints
CHOP		CHOP
HMM_to_HH		HMM_to_HH
L5_NewTTPC_notWorking		L5_NewTTPC_notWorking
Neuron_Model_HMM		Neuron_Model_HMM
Neuron_Model_HMM_with_young		Neuron_Model_HMM_with_young
Neuron_general		Neuron_general
Plots_Folder		Plots_Folder
StableL5		StableL5
StableL5_naHMM		StableL5_naHMM
TAU		TAU
UDB20		UDB20
csv_files		csv_files
final_draft		final_draft
mechs		mechs
obsolete		obsolete
restructuring		restructuring
slurm		slurm
x86_64		x86_64
#Optimization_HHtoHMM_rel.py#		#Optimization_HHtoHMM_rel.py#
.DS_Store		.DS_Store
.HMM_plotter.py.swp		.HMM_plotter.py.swp
.Optimization with New Protocol.py.swp		.Optimization with New Protocol.py.swp
.generalized_genSim_shorten_time.py.swp		.generalized_genSim_shorten_time.py.swp
.gitattributes		.gitattributes
.gitignore		.gitignore
.scoring_functions_exp.py.swp		.scoring_functions_exp.py.swp
.swp		.swp
.vclamp_evaluator_HMM.py.swo		.vclamp_evaluator_HMM.py.swo
.vclamp_evaluator_HMM.py.swp		.vclamp_evaluator_HMM.py.swp
GeneralChangeParameters.py		GeneralChangeParameters.py
HMM_plotter.py		HMM_plotter.py
Optimization with Evaluator.ipynb		Optimization with Evaluator.ipynb
Optimization with New Protocol.ipynb		Optimization with New Protocol.ipynb
Optimization with New Protocol.py		Optimization with New Protocol.py
Optimization_HHtoHMM.ipynb		Optimization_HHtoHMM.ipynb
Optimization_HHtoHMM_exp.py		Optimization_HHtoHMM_exp.py
Optimization_HHtoHMM_plotter_demo.ipynb		Optimization_HHtoHMM_plotter_demo.ipynb
Optimization_HHtoHMM_rel.py		Optimization_HHtoHMM_rel.py
Parameter Change.ipynb		Parameter Change.ipynb
Parameter_Changer_Test_Notebook.ipynb		Parameter_Changer_Test_Notebook.ipynb
Plot_opt_results.ipynb		Plot_opt_results.ipynb
Readme.txt		Readme.txt
SCN2A_nb_helper_actinact.py		SCN2A_nb_helper_actinact.py
Testing Generate Simulation.ipynb		Testing Generate Simulation.ipynb
cp.pkl.tmp		cp.pkl.tmp
curve_fitting.py		curve_fitting.py
drive.sh		drive.sh
drive_rbs.sh		drive_rbs.sh
eval_helper.py		eval_helper.py
eval_helper_na12.py		eval_helper_na12.py
eval_helper_na12mut.py		eval_helper_na12mut.py
eval_helper_na12mut8st.py		eval_helper_na12mut8st.py
eval_helper_na16.py		eval_helper_na16.py
fitting_na_16.ipynb		fitting_na_16.ipynb
fitting_na_16_plotter.ipynb		fitting_na_16_plotter.ipynb
genSimData_Na12ShortenTime.py		genSimData_Na12ShortenTime.py
general_plotter.py		general_plotter.py
generalized_genSim_shorten_time.py		generalized_genSim_shorten_time.py
generalized_genSim_shorten_time_HMM.py		generalized_genSim_shorten_time_HMM.py
generalized_genSim_shorten_time_HMM_old.py		generalized_genSim_shorten_time_HMM_old.py
generalized_genSim_shorten_time_old.py		generalized_genSim_shorten_time_old.py
generate_simulation.py		generate_simulation.py
hof.pkl		hof.pkl
hofbest_indv.pkl		hofbest_indv.pkl
indv.pkl		indv.pkl
indvbest_indv.pkl		indvbest_indv.pkl
jan.txt		jan.txt
jinan_test.pdf		jinan_test.pdf
log.pkl		log.pkl
na16.mod		na16.mod
optimize_na_ga.py		optimize_na_ga.py
optimize_na_ga_v2.py		optimize_na_ga_v2.py
plot_all_protocols_hmm.py		plot_all_protocols_hmm.py
plotter_helper.py		plotter_helper.py
sbatch.sh		sbatch.sh
sbatch_rbs.sh		sbatch_rbs.sh
scalebary.py		scalebary.py
scoring_functions.py		scoring_functions.py
scoring_functions_exp.py		scoring_functions_exp.py
scoring_functions_relative.py		scoring_functions_relative.py
state_variables.py		state_variables.py
temp_results.txt		temp_results.txt
test.pdf		test.pdf
vclamp_evaluator.py		vclamp_evaluator.py
vclamp_evaluator_HMM.py		vclamp_evaluator_HMM.py
vclamp_evaluator_HMMtoHH.py		vclamp_evaluator_HMMtoHH.py
vclamp_evaluator_relative.py		vclamp_evaluator_relative.py

Repository files navigation


An automated modeling platform to simulate SCN2A and SCN8A variants' effects in pyramidal neurons.





Notes:

Versions listed oldest to most recent:
genSimData_Na12.py, genSimData_Na12_mut_new_parallel.py, 
	genSimData_Na12ShortenTime.py, generalized_genSim_shorten_time.py



References:

conductance calculation formulas:
	DOI: https://doi.org/10.1016/j.biopsych.2017.01.009
		--supplement 1, page 2 (Electrophysiology) for peak current Boltzmann and norm. conductance equations



Installation:
With conda do:
conda install -c conda-forge neuron