Publication dateSep 19, 2024
Confidentiality public Public
Generate Bioprocess Demo Data
TASK
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:
- Info CSV: One row per sample with Batch, Fermentor, Medium, and experimental conditions
- Medium CSV: One row per unique medium with mean composition columns
- Raw Data CSV: Synthetic time-series measurements (Biomasse, pH, temperature, NaOH) correlated with growth
- 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)
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Input
Metadata Feature Table
Merged metadata-feature table with Series, medium composition, conditions, and model parameters
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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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