vgrampy

Author: Caleb Nejely ( Adapted from Noel Lefevre (Adapted from Steven Ramsey's LDNH README.md)))

Date: August 7, 2025

Installing Vgram

You Must have Python, git, and visual studio code installed. Tested and working on python 3.9.x, may work on newer versions. If you do not have git installed you may instead download the code as a .zip from github, extract, and open the folder in visual studio code

1. Clone the repository

cd <file path where you want the code to clone to>
git clone https://github.com/ramseylab/vgrampy.git -b "GUI"
cd Vgram_UI

2. Install dependencies

   • If you only have one version of python installed

   pip install -r requirements.txt

   • If you have more than one version of python (version X.Y)

   pythonX.Y -m pip install -r requirements,txt

3. Open Vgram_UI folder in visual studio code

4. Open UI.py

5. Use the play button in the top right to run

   If you have multiple python versions first select an interpreter using the button on the bottom right

Options for Vgram:

There are default parameters applied, but you can change them if needed

• Plot Data: generate automatic plots of the data

• Seperate Concentrations: seperate plots based on concentration in the file name

• Transform Data: rotates and cleans up the output dataframe for easier work in excel, add an additional output file

• Seperate Conditions: seperates data into folder before analysis based on the fourth item in the file name (eg. condition in "YYYY_MM_DD_<Condition (optional)>")

• Do log input: log-transform or not (default 'yes')

• Peak Feature: peak curvature, height or area (default = peak curvature)

• Start Voltage: voltage start point of data (default = 0.852 for carbamazepine, change to 0.952 for oxcarbazepine)

• Analyate Code: code for drug of intrest (cbz for carbamazepine, oxc for oxcarbazepine)

• Smoothing: amount of smoothing the voltammogram (default = 0.006)

• Stiffness: how strictly the spline passes through the data points (default = 0)

• Vwidth: voltage width to window out when making the spline (default = 0.15)

• Peak Voltage Range: voltage range to look for the peak in (default = 1.0 to 1.1)

Plotting In Vgram:

You can choose whether or not to plot, and whether to separate those plots by concentration

The plots saved will be the smoothed and detilted voltammograms

Output Files

There are 3 files created by running the installed program by default

The naming convention for each file is: [filename]_[log or no log]_[smoothing parameter]_[stiffness parameter]_[window width] For example dataframe_log_curvature_0.006_0_0.15.xlsx

1. A dataframe excel file that has each replicates' data:

conc	replicate	V	I	logI	smoothed	detilted
0	1	0.504	0.08379	-0.25515	-0.24431	0
0	1	0.508	0.8375	-0.25584	-0.23192	0
0	1	0.512	0.8564	-0.21048	-0.21048	0
0	1	0.516	0.8797	-0.18492	-0.18001	0
0	1	0.520	0.9069	-0.14098	-0.14420	0

2. A signal excel file that has the signal, peak voltage, and voltage center for each replicate:

file	signal	peak V	vcenter
2024_01_02_cbz00_01.txt	23.9020	1.083	1.012
2024_01_02_cbz15_01.txt	324.8372	1.074	1.076
2024_01_02_cbz15_02.txt	236.3741	1.061	1.064

3. A stats excel file that has the signal, peak voltage, and voltage center for each replicate:

conc	average	std	CV	T-Statistic	avg peak	std peak
0.0μM	28.9	20.11	0	0	1.02	0.04
5.0μM	84.11	14.19	0.169	6.34	1.06	0.01
10.0μM	9.80	29.8	0.206	5.19	1.07	0
15.0μM	227.97	42.43	0.186	4.54	1.07	0