Engin Strain-to-Scale
One Engin project file in; which host, which route and which runs to do next, each with a 90% band, merged into one decision brief.
by Temple Compute
Run Engin Strain-to-Scale on Horus
W-42 · Engin Strain-to-Scale
One Engin project file in; which host, which route and which runs to do next, each with a 90% band, merged into one decision brief.
Domain: Omics
Overview
Engin answers three questions for early bioprocess development, each with a calibrated 90% band: which host (engin-host), which route (engin-pathway) and what to run next (engin-process). The three stages read the same project.yaml and are independent, so they run in parallel and a summary task merges them into one decision brief that keeps every interval and caveat. Engin intervals land near nominal 90% coverage on 406 real fermentation batches, but its point predictions are weak (R² ≈ 0.02-0.11). The workflow has 4 tasks.
Pipeline
project.yaml
┌────────────────┼────────────────┐
▼ ▼ ▼
host (chassis) pathway (route) process (next runs)
└────────────────┼────────────────┘
▼
summary (results/summary.{json,md})
Inputs / Outputs
- Input:
examples/project.yaml, read by all three stages. Every section is optional. results/host.{json,txt}: ranked host organisms with recommendation and 90% band.results/pathway.{json,txt}: ranked biosynthetic routes with manufacturability intervals.results/process.{json,txt}: current best cost and next runs ranked by expected cost reduction.results/summary.{json,md}: merged decision brief.examples/expected-output/: captured reference run (seed: 0) of the three stages.
Parameters
| id | Default | Meaning |
|---|---|---|
| project | examples/project.yaml | Engin project file read by all three stages |
Settings live in the project file: host.weights / host.hard, pathway.routes, process.reactor, process.cost (default target $200/kg), process.batch_size (4) and seed (0).