Record the reactor, not the precultures beside it (#183) - #534
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Clostridium_Ljungdahlii_Kluyveri_Syngas_Alcohol_Coculture: a 2 L Biostat M at 1 L working volume, 37 °C by water jacket, pH controlled by KOH, agitation raised from 200 to 400 rpm at hour 475, fed continuously with syngas (60% CO, 35% H2, 5% CO2) recirculated through the headspace. Two judgements are recorded rather than assumed. The mode is CONTINUOUS, not CHEMOSTAT, even though the vessel is sold as a chemostat and the paper calls it one. Cells were retained, giving a bleed rate of a quarter of the applied dilution rate, so biomass is not washed out at the dilution rate and the defining property of a chemostat does not hold. What the equipment is called is not evidence about how it was run. feed_or_dilution_rate is unset: 80 mL/h in Phase 1, 40 mL/h in Phases 2-5, and the phases are the experiment. A single value would assert a steady state the paper does not claim — the same call made for the thiocyanate retention time and the Caldicellulosiruptor dilution sweep. The same paper carries serum-bottle conditions — 160 mL bottles, 10 to 50 mL working volume, 35 °C — and none of them are here. Those are the two strains' separate precultures. Recording them as the community's setup is exactly the error #529 was filed for, and this record is where that guard first had something to be careful about. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Network integrity findingsWarnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build. The full report is attached to the workflow run as an artifact. |
This was referenced Aug 11, 2026
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What
Clostridium_Ljungdahlii_Kluyveri_Syngas_Alcohol_Coculture— a 2 L Biostat M at 1 L working volume, 37 °C by water jacket, pH controlled by KOH, agitation raised 200 → 400 rpm at hour 475, fed continuously with syngas (60% CO, 35% H₂, 5% CO₂) recirculated through the headspace.Two judgements recorded rather than assumed
The mode is
CONTINUOUS, notCHEMOSTAT— even though the vessel is sold as a chemostat and the paper calls it one. Cells were retained, giving a bleed rate of a quarter of the applied dilution rate, so biomass is not washed out at the dilution rate and the defining property of a chemostat does not hold. What the equipment is called is not evidence about how it was run, and the snippet supporting this is the bleed-rate sentence rather than the vessel name.feed_or_dilution_rateis unset. It was 80 mL/h in Phase 1 and 40 mL/h in Phases 2–5, and those phases are the experiment. A single value would assert a steady state the paper does not claim — the same call made for the thiocyanate retention time and the Caldicellulosiruptor dilution sweep.What was deliberately not taken from the same paper
It also carries serum-bottle conditions: 160 mL bottles, 10/20/50 mL working volume, 35 °C. None of them are here. Those are the two strains' separate precultures, not the coculture.
That is the error class #529 was filed for one PR ago — a rich methods section attached to the wrong organism. This record is the first where the guard had something to actually be careful about: the paper passes the member-coverage check at 100%, so the automated signal is green, and the discrimination still has to be made by reading. The guard narrows what needs reading; it does not replace it.
Checks
just validate— no issuesjust validate-references— 0 issues; all three snippets verbatimjust validate-strict,just lint,just check-docs-current— exit 0uv run pytest tests/— 2375 passed, 16 skippedPart of #183.
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