JupyterNotebooksDEGENaCPharm

Jupyter notebooks create figures for amplitude data (change in current and ratio) and selectivity data (relative permeability) from TEVC data. There are two folders: 1) containing the figures for the Fechner et al. 2021, JGP paper and 2) figures to analyze data from N-terminal mutation study project. FOr the Dose response figures, data were analyzed with IgorPro, Individual dose-response curve fitted with the HIll equation and the fitted values for IC50 and EC50 entered into excel data shets.

Make Figures from TEVC data

• Analyze data with TEVC Matlab code
• Run RatioNterm notebook for amplitude measurement
• Run Selectivity-Nterm-Data notebook for calculating the relative permeability

Analyze data with TEVC Matlab code

• Follow the description to analyze TEVC amplitude with TEVCAnalyzeLoopSTFX.m and selectivity with TEVCSelectivitySTFX.m

Figure creating with Jupyter notebook:

• Clone jupyter notebook to your computer:
  • https://github.com/wormsenseLab/JupyterNotebooksDEGENaCPharm.git
  • Contains analysis files for paper Fechner et al. 2021 and Nterm project
  • You have to make sure that the dabest package is installed for estimation plots
• Navigate into folder on your computer via terminal
• Enter jupyter notebook in terminal

Run RatioNterm notebook for amplitude measurement

• Folder path are absolute (unfortunately), so, if you have my analysis folder TEVC-GoodmanlabBOX and kept everything structured the same, you only need to change the variable mypath
• listofFiles = define the “frogs” you want to include in the analysis, e.g. STFX111, STFX112; just enter 111 and 112; STFX will be concatenated to the string automatically
• if you want to change the order or the constructs you want to plot, change the variables:
  • ReNameAlanin which plots all individual alanine mutation constructs
  • ReNameChimera which plots all individual chimera constructs
  • ReNameChimeraHet which plots the heteromeric data
• filedirExportFig gives the path where it exports the figures

Run Selectivity-Nterm-Data notebook for calculating the relative permeability

Package requirement

• Python XX
• dabest

Add heka_reader to PYTHONPATH

import sys fpath = '/Users/Fechner/Dropbox/PythonImport/heka_reader' #MAC sys.path.append(fpath) import heka_reader

got the heka reader from here

Heka Reader

• clone the repository to your computer (move to directory with terminal commands. Mine here is called PythonStuff at the moment: change name)
  • git clone https://github.com/campagnola/heka_reader.git
• the heka reader enables to read and access the .dat files (to work in jupyter notebook, you habe to append the heka_reader to the path where the heka reader is stored)
• browser.py enables to easily browse for recordings within a .dat comparable to Igor or other similar programs
• I changed the following in my local browser.py version, because the functions output was a tuple:
  • def load_clicked():
  • Display a file dialog to select a .dat file
  • file_name = pg.QtGui.QFileDialog.getOpenFileName()
  • if isinstance(file_name, tuple): (ADDED THIS LINE)
    • file_name = file_name[0] (ADDED THIS LINE)
  • if file_name == '':
    • return
  • load(file_name)

Brief example for heka_reader: we changed

*Load a .dat file
bundle = Bundle(file_name)

*Select a trace
trace = bundle.pul[group_ind][series_ind][sweep_ind][trace_ind]

*Print meta-data for this trace
print(trace)

*Load data for this trace
data = bundle.data[group_id, series_id, sweep_ind, trace_ind]