ClpXP Control Module: Deployment in Nucleus Cytosol

Yen-Yu Hsu

doi:10.63765/xxre8785

Setup

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

Analyze time-series fluorescence data from PURE (Protein synthesis Using Recombinant Elements) experiments.

Setup¶

%load_ext autoreload
%autoreload 2
    
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt

from cdk import logging
log = logging.setup_logging(logging.ERROR)

# Import the cdk platereader module
# from cdk.analysis.cytosol import platereader as pr
import cdk.instruments.platereader as pr

Load Data¶

# Specify file paths
data_file = "20260604-113617-cytation5-pure-timecourse-gfp.txt"
platemap_file = "new-platemap.csv"


# Load data
result = pr.load_platereader_data(
    data_file=data_file,
    platemap_file=platemap_file,
    platereader="biotek"  # Options: "cytation", "envision", "biotek-cdk"
)

# Checkout first few rows
print(result)

[06/15/26 14:04:38] INFO     Found 1 plate blocks                  biotek.py:105
                    INFO     Parsing plate block 1                 biotek.py:112
                    INFO     Read metadata section, found 2 read   biotek.py:213
                             block(s).                                          
                    INFO     Parsed 2 segment(s) successfully.     biotek.py:466
                    INFO     Found 0 segment(s) that could not be  biotek.py:467
                             associated with existing read data.                
                    WARNING  Platemap 'Type' column contains     platemap.py:141
                             unexpected values: ['Control'].                    
                             Expected one of: ['Blank',                         
                             'Negative Control', 'Positive                      
                             Control', 'Sample', 'Standard'].                   
PlateReaderResult with the following 2 blocks:
0: (876, 38) kinetic read with reads: GFP-G70:485,528 (Fluorescence) (Plate 'Plate 1')
1: (876, 38) kinetic read with reads: GFP-Gext:485,528 (Fluorescence) (Plate 'Plate 1')

data = result[1]

Plot Raw Curves¶

#g = data.plot(style='Type')
g = data.plot()
g.savefig('raw', dpi=300)