PPK Module testing in PURE

Surendra Yadav

doi:10.63765/djnv7772

Analysis: 20250610

!pip install nucleus-cdk==0.5.0rc2 | tail -n2

Requirement already satisfied: asttokens in /opt/homebrew/anaconda3/lib/python3.12/site-packages (from stack-data->ipython>=6.1.0->ipywidgets==8.*->jupyter-bokeh<5.0.0,>=4.0.5->nucleus-cdk==0.5.0rc2) (2.0.5)
Requirement already satisfied: pure-eval in /opt/homebrew/anaconda3/lib/python3.12/site-packages (from stack-data->ipython>=6.1.0->ipywidgets==8.*->jupyter-bokeh<5.0.0,>=4.0.5->nucleus-cdk==0.5.0rc2) (0.2.2)

import matplotlib.pyplot as plt
from cdk.analysis.cytosol import platereader as pr
import warnings

warnings.filterwarnings('ignore')
pr.plot_setup()

data, platemap = pr.load_platereader_data("./data/20250610-161953-cytation5-pure-timecourse-gfp-ppk-controls-2-biotek-cdk.txt", "20250610-ppk-energy-solution-platemap.csv")

data

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g = pr.plot_curves(data, palette="colorblind")
g.savefig("plot1")

s = pr.plot_steadystate(data, palette="colorblind")
plt.xlabel('Condition')
s.savefig("plot2")

pr.plot_kinetics(data)

PROVIDING AVERAGED KINETICS

(<seaborn.axisgrid.FacetGrid at 0x146859e50>,
                                         Velocity                      \
                                             Time      Data       Max   
 Name          Read                                                     
 ES + CP       GFP-Gext 0 days 01:39:31.938945422 166833.99 161361.42   
 ES - CP       GFP-Gext 0 days 02:18:43.416395225    836.54    241.09   
 PURE Positive GFP-Gext 0 days 01:15:16.816069328 725591.90 964744.54   
 
                                                Lag           \
                                               Time     Data   
 Name          Read                                            
 ES + CP       GFP-Gext   0 days 00:36:03.955438422 19440.01   
 ES - CP       GFP-Gext -1 days +22:43:56.496117396   379.35   
 PURE Positive GFP-Gext   0 days 00:30:10.731839295 73898.46   
 
                                     Steady State             \
                                             Time       Data   
 Name          Read                                            
 ES + CP       GFP-Gext 0 days 03:12:58.126479814  316984.58   
 ES - CP       GFP-Gext 0 days 07:34:55.791588130    1589.42   
 PURE Positive GFP-Gext 0 days 02:21:40.766012752 1378624.62   
 
                                                                       Fit  \
                                                                    params   
 Name          Read                                                          
 ES + CP       GFP-Gext  [333667.9829118206, 1.9067328438836142, 1.6588...   
 ES - CP       GFP-Gext  [1673.0712098104584, 0.5679043393477711, 2.312...   
 PURE Positive GFP-Gext  [1451183.8070235197, 2.661025429537054, 1.2546...   
 
                                       
                         R^2    drift  
 Name          Read                    
 ES + CP       GFP-Gext 1.00  7171.30  
 ES - CP       GFP-Gext 0.97  -149.87  
 PURE Positive GFP-Gext 1.00 30037.30  )

pr.kinetic_analysis(data)

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