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Flag translation collapse on the card: ribosome_elongation_rate_mean < 1 aa/s

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README.md re-rendered with card.render: an Outcomes paragraph after the QC crosswalk states Cellarium's translation_collapse predicate (mean ribosome elongation rate below 1 aa/s) as ribosome_elongation_rate_mean < 1 in the summary config: 6,273 trajectories, 4,188 of them with termination_class none. manifest.json gains translation_collapse (per family counts).

Files changed (2) hide show
  1. README.md +3 -1
  2. manifest.json +1 -1
README.md CHANGED
@@ -255,7 +255,9 @@ The same outcomes in the `qc` vocabulary of the Cellarium corpus:
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  | `equilibrium_unstable` | `crashed` | equilibrium solver failure |
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  | `other` | `crashed` | any other simulator error |
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- Only `time_limit` is a prediction of the model about the cell; the other non-`none` classes are numerical failures of the simulation, and a viability task should treat them as such. Cellarium's `implausible_channel`, `over_replicated` and `translation_collapse` have no counterpart here because well4cell does not run those checks; its vocabulary is defined in the Cellarium repository's `docs/QC_STATUSES.md` (https://github.com/evanniko1/cellarium).
 
 
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  ## Suggested tasks
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  | `equilibrium_unstable` | `crashed` | equilibrium solver failure |
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  | `other` | `crashed` | any other simulator error |
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+ Only `time_limit` is a prediction of the model about the cell; the other non-`none` classes are numerical failures of the simulation, and a viability task should treat them as such. Cellarium's `implausible_channel` and `over_replicated` have no counterpart here because well4cell does not run those checks; its vocabulary is defined in the Cellarium repository's `docs/QC_STATUSES.md` (https://github.com/evanniko1/cellarium).
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+
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+ A generation can divide while its ribosomes have effectively stopped, because chromosome replication does not require ongoing translation. The Cellarium corpus flags this as `translation_collapse` when the mean ribosome elongation rate over the generation is below 1 aa/s, an order of magnitude below the slowest elongation rate measured in *E. coli* (Dai et al. 2016). The same predicate on this dataset is `ribosome_elongation_rate_mean < 1` in the `summary` config. It flags 6,273 trajectories in this release, 4,188 of them with `termination_class` `none` (divided, but with translation collapsed). Treat them as inviable in any viability task.
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  ## Suggested tasks
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manifest.json CHANGED
@@ -1 +1 @@
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+ {"active_columns": {"exchange_flux_matrix": {"active": 82, "columns": 87}, "mrna_counts_matrix": {"active": 2773, "columns": 3133}, "protein_counts_matrix": {"active": 4174, "columns": 4310}, "reaction_flux_matrix": {"active": 3974, "columns": 9612}}, "built_at": "2026-10-09T17:33:51+00:00", "configs": {"core": {"bytes": 18594865271, "families": {"double_knockout": {"bytes": 1863842291, "files": 1, "rows": 31390535, "trajectories": 11951}, "dynamic_media": {"bytes": 2774609830, "files": 2, "rows": 47151419, "trajectories": 18599}, "regulation": {"bytes": 323918365, "files": 1, "rows": 5501785, "trajectories": 2046}, "single_knockout": {"bytes": 13529451993, "files": 7, "rows": 230981330, "trajectories": 83937}, "wildtype_media": {"bytes": 103042792, "files": 1, "rows": 1726776, "trajectories": 641}}, "files": 12, "rows": 316751845, "stride": 1, "trajectories": 117174}, "expression": {"bytes": 512443776, "families": {"wildtype_media": {"bytes": 512443776, "files": 1, "rows": 173523, "trajectories": 641}}, "files": 1, "rows": 173523, "stride": 10, "trajectories": 641}, "metabolism": {"bytes": 502291146, "families": {"wildtype_media": {"bytes": 502291146, "files": 1, "rows": 173523, "trajectories": 641}}, "files": 1, "rows": 173523, "stride": 10, "trajectories": 641}, "summary": {"bytes": 29622524, "families": {"double_knockout": {"bytes": 3356859, "files": 1, "rows": 11951, "trajectories": 11951}, "dynamic_media": {"bytes": 5235412, "files": 1, "rows": 18599, "trajectories": 18599}, "regulation": {"bytes": 622968, "files": 1, "rows": 2046, "trajectories": 2046}, "single_knockout": {"bytes": 20202224, "files": 1, "rows": 83937, "trajectories": 83937}, "wildtype_media": {"bytes": 205061, "files": 1, "rows": 641, "trajectories": 641}}, "files": 5, "rows": 117174, "stride": 1, "trajectories": 117174}}, "failed_jobs": {"failed_jobs": 971, "with_generations": 920}, "families": {"double_knockout": {"cells": 375, "lineages": 3000, "trajectories": 11951}, "dynamic_media": {"cells": 684, "lineages": 5472, "trajectories": 18599}, "regulation": {"cells": 64, "lineages": 512, "trajectories": 2046}, "single_knockout": {"cells": 2752, "lineages": 21949, "trajectories": 83937}, "wildtype_media": {"cells": 21, "lineages": 168, "trajectories": 641}}, "git_commit": "60e68057b55926b0771cbb5c788e55a00805ef40", "git_dirty": false, "held_back": [], "kb_sha256": {"5558948af4ad806f21d7c80c": "8ff93a58576f484edfd6fea641eeeb4fc554b52b97da49f4d8b275ca74496667", "fa6a9ebd4b1c988a36ef9fa1": "b1750cf04409c37ebce9d4d3009daeae0779dd66508812c2807744d83baf1ab7"}, "qc": {"attempts": 118456, "failed": 0}, "termination_class": {"equilibrium_unstable": 6, "fba_infeasible": 3, "negative_counts": 2647, "none": 112545, "time_limit": 1973}, "trajectories": 117174, "translation_collapse": {"divided": 4188, "families": {"double_knockout": {"divided": 158, "trajectories": 201}, "dynamic_media": {"divided": 1027, "trajectories": 1602}, "regulation": {"divided": 0, "trajectories": 0}, "single_knockout": {"divided": 3003, "trajectories": 4470}, "wildtype_media": {"divided": 0, "trajectories": 0}}, "threshold_aa_per_s": 1.0, "trajectories": 6273}, "version": "1.0.0-rc1"}