SIHUMIx: chemostat, and three fields left empty on purpose (#183) - #535
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SIHUMIx: chemostat, and three fields left empty on purpose (#183)#535realmarcin wants to merge 1 commit into
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In vitro bioreactors run chemostatically on complex intestinal medium, held anaerobic by continuously gassing the vessels with nitrogen, 250 mL. Each of the eight species is grown alone for 72 h first and the reactor inoculated with 1e9 cells of each, so the community starts from a defined, equal-per-strain inoculum rather than a mixed culture — worth recording because it is what makes SIHUMIx reproducible between labs. What is not recorded matters as much here. system_type is BIOREACTOR_UNSPECIFIED. The paper says "in vitro bioreactors" and points at prior work for the design; it never says stirred-tank. Guessing the vessel would put an unevidenced enum value where a reader takes it as read from this paper. operating_temperature is absent. The 37 °C and 175 rpm in this paper attach to strains "cultivated separately" in BHI — the eight precultures, not the community. That is the second record running where the same paper carries preculture conditions next to the community's, which is the pattern #529 names; the bioreactor's own temperature lives in the cited prior study. The 250 mL is flagged in notes as the medium volume the inoculum went into. It is the closest thing the source offers to a working volume and the source does not call it one. 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
SIHUMIx_Human_Intestinal_Model_Community— in vitro bioreactors run chemostatically on complex intestinal medium, held anaerobic by continuously gassing the vessels with nitrogen, 250 mL.Each of the eight species is grown alone for 72 h, then the reactor is inoculated with 1×10⁹ cells of each. That is in
instrument_detailbecause it is what makes SIHUMIx reproducible between labs — the community starts from a defined, equal-per-strain inoculum rather than from a mixed culture.Three fields left empty, each for a stated reason
system_typeisBIOREACTOR_UNSPECIFIED. The paper says "in vitro bioreactors" and points at prior work for the design. It never says stirred-tank. Guessing the vessel would put an unevidenced enum value where a reader takes it as read from this paper.operating_temperatureis absent. The 37 °C and 175 rpm in this paper attach to the sentence about strains "cultivated separately" in BHI — those are the eight precultures, not the community. The bioreactor's own temperature is in the cited prior study.This is the second record running where the same paper carries preculture conditions sitting next to the community's, which is the pattern #529 names. Both times the automated member-coverage check was green (this source names 8 of 8 members), and both times the discrimination came from reading the sentence the number attaches to. The guard narrows what needs reading; it doesn't replace it.
working_volumecarries a caveat innotes. The 250 mL is the medium volume the inoculum went into — the closest thing the source offers, and the source does not call it a working volume.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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