Chapter 5 reductive-amination HTE screen

This repository packages the code and processed outputs used for the reductive-amination high-throughput screen described in Chapter 5 of the thesis. It is intended as a reproducible research-code companion, with raw instrument data shared separately through the approved data-access route.

Contents

protocols/           OT-2 setup and dilution protocols (Opentrons API 2.19)
notebooks/           parsing and modelling walkthroughs
data/processed/      source-derived parsed data and reported modelling outputs
data/examples/       small integration-summary export fixtures
data/raw/            documented location for authorised external exports
figures/             example peak-picked integration-summary figures
scripts/             figure renderer
tests/               dependency-light repository checks
docs/                validation environment details

Quick start

Create a Python environment, install the analysis dependencies, then start Jupyter from the repository root.

python -m pip install -r requirements.txt
python -m unittest discover -s tests -v
jupyter lab

Run notebooks/01_parse_hplc.ipynb to inspect the parsing workflow and notebooks/02_model_hte.ipynb to inspect the modelling inputs and reported outputs. Both use paths relative to the repository root.

Data availability

data/processed/parsed_hplc_data.csv and data/processed/model_outputs.csv are the source-derived tables used for the reader-facing notebooks. The full peak-picked integration-summary exports belong in data/raw/hplc_exports/ when an authorised user needs to regenerate the parsed table. Vendor .raw chromatogram directories are not versioned.

The example figures visualise selected peak identity, retention time, and integrated area from the integration-summary exports. They are not detector time-series chromatograms.

See data/processed/DATA_DICTIONARY.md for the tracked-table fields and docs/ENVIRONMENT.md for the validation environment.

OT-2 protocols

The setup and dilution protocols retain source-supported transfer logic and use Opentrons API level 2.19. Review the deck map, reagent identities, stock concentrations, plate positions, run parameters, and laboratory safety requirements in the Opentrons App before an experimental run. These details remain author-controlled because the protocol sources alone do not establish all of them.

Reproduce the figures

After dependencies are installed, run:

python scripts/render_peak_pick_examples.py

This rebuilds the tracked SVG figures from the small example export fixtures.