Vendor cytotoxicity data that scientists hand-normalised became a validated pipeline with QC flags, a one-click IC50 curve generator and a 71-assay automation roadmap.
Flag, don't fix. The pipeline never corrects a value — it surfaces the ones a scientist should look at. Slower on paper, trusted in practice, and the reason it got used.
— The call I madePBMC cytotoxicity results arrived from the CDMO as CSV and XLSX files that disagreed with each other about units, column names and layout. Scientists normalised them by hand, computed IC50s in ad-hoc spreadsheets, and nothing traced a processed number back to the raw row it came from.
It worked, in the way that a careful person doing it every time works — right up until the day someone else had to do it, or a reviewer asked where a number came from.
The processing scripts validate the schema, normalise units, detect outliers, average across donors and flag anything that needs a human eye — then write Scispot-ready outputs and keep Raw and Processed databases in Notion so every row is traceable. An interactive IC50 generator turns processed data into dose-response curves with per-donor variability in one click. The first working version ran on one real CDMO file in front of the science team before any roadmap existed.
Every value is traceable to its raw row; the scientist decides what a flag means.
| Row | Flag | Why | Scientist's call |
|---|---|---|---|
| D2 · 12 nM | Outlier | Viability 61% vs donor-mean 44% at this dose; 2.3 SD from the curve. | Kept — replicate well confirmed; noted in run log. |
| D3 · 200 nM | Unit | Column reported µg/mL where the template expects nM; converted using the stated MW. | Accepted conversion after checking the CDMO sheet. |
| D1 · 0.01 nM | Baseline | Top plateau 103%; clamped for fitting, raw value preserved. | No change. |
A batch that took [X hours] of re-keying now takes minutes of reviewing flags, and every processed value points back to raw data. The IC50 view that used to be an afternoon in a spreadsheet is one click. [METRIC: assays automated to date] of the 71 on the roadmap are live.
A working prototype on one real CDMO file, demoed to the science team before any roadmap existed. Then weekly with the lab lead, with tickets written tightly enough that engineering shipped without a re-spec.
— How it came together