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Sep 19, 2024

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Generate Bioprocess Demo Data

TASK
4 times
100 %
633 milliseconds
Typing name :  TASK.gws_plate_reader.GenerateBioprocessDemoData Brick :  gws_plate_reader

Generate demo input files for the Bioprocess app from a metadata-feature table

Generate demo input files for the Constellab Bioprocess app.

This task takes a metadata-feature table (typically the output of CellCultureMergeFeatureMetadata) and generates the 4 input files required by ConstellabBioprocessLoadData:

  1. Info CSV: One row per sample with Batch, Fermentor, Medium, and experimental conditions
  2. Medium CSV: One row per unique medium with mean composition columns
  3. Raw Data CSV: Synthetic time-series measurements (Biomasse, pH, temperature, NaOH) correlated with growth
  4. Follow-up ZIP: Synthetic OD growth curves generated from logistic 4P model parameters (online monitoring)

Input Table Structure

The input table must have:

  • Series column: sample identifier in format <Batch>_<Fermentor> (e.g., "M1_1")
  • Medium column: medium name
  • Medium composition columns (numeric, positioned before condition columns)
  • Condition columns (e.g., "T ( C)", "pH (u_pH)", "OD at 880 nm", "NaOH (mL)")
  • Model column (or param_* columns): marks the boundary between metadata and features
  • param_y0, param_A, param_mu, param_lag: logistic 4P model parameters

Column Detection

  • Metadata columns: all columns between Medium and Model (or first param_* column)
  • Composition columns: metadata columns before the first one containing parentheses
  • Condition columns: metadata columns from the first one containing parentheses onward

Generated Data

  • Raw data: Biomasse (g/L) from logistic 4P model (offline measurements every 2h), pH decreases with growth, NaOH increases cumulatively, temperature stays constant (with noise)
  • Follow-up: OD at 880 nm from logistic 4P model (online monitoring every 0.5h, with noise)

Input

Metadata Feature Table
Merged metadata-feature table with Series, medium composition, conditions, and model parameters

Output

Info CSV file
CSV with Batch, Fermentor, Medium, and experimental conditions
Raw data CSV file
CSV with synthetic time-series measurements per sample
Medium CSV file
CSV with medium composition (one row per unique medium)
Follow-up ZIP file
ZIP containing synthetic OD growth curve CSVs per sample
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