evanniko1/cellarium-corpus

Cellarium Corpus

A distilled, queryable corpus of whole-cell Escherichia coli simulations produced with the Covert Lab wcEcoli model, plus (optionally) the full raw trajectories. It is the data layer behind Cellarium — a grounded agent + Socratic-council that answers whole-cell questions strictly from these results.

Two tiers

Tier	What	Where	Size
Manifest (always here)	Per-(design, seed) distilled summaries: QC verdict, viability, summary-channel means + downsampled trajectories, per-media-segment means, pathway proteome fractions, and a 199-species panel (terminal count + coarse trajectory)	data/manifest/*.parquet	~MB
Raw (optional)	Full simOut trajectories per run, one .tar.gz per lineage	runs/cellarium/<variant>/<seed>.tar.gz	~GBs each

The manifest answers most questions (panel species, summary channels, viability) with no download. Reach for a raw archive only when you need an arbitrary (non-panel) species, full timestep resolution, or FBA fluxes.

Load the manifest

from datasets import load_dataset
ds = load_dataset("evanniko1/cellarium-corpus", "manifest")   # the distilled corpus
# or directly with DuckDB / pandas over data/manifest/*.parquet

Key columns: perturbation, condition, timeline, seed, elongation_model, qc, reportable, generations, crashed, crash_type, division_rate, gens_reached, channels (means), channel_stats, series (downsampled), pathways, species_panel (per-monomer {mean, last, series}), simout_path.

elongation_model — filter on this before pooling anything tRNA-related

The model tree carries three translation-elongation models, and the same column name means a different quantity under each. elongation_model records which one produced a row; a row without it (written before the column existed) is steady_state, which is known rather than assumed — no earlier run could select another model.

value	what it does	fraction_trna_charged (86 wide in all three)
steady_state	charging solved as a 20-state ODE indexed by amino acid, then broadcast across the family	21 distinct values in 86 columns; within-family spread is 0.00 by construction, not a measurement
kinetic	per-isoacceptor charging with explicit codon reading (Choi & Covert 2023)	86 genuinely independent values
coarse_kinetic	coarse-grained elongation that does not solve charging at all	86 exact zeros — the absence of a model, not total de-acylation

So: never average fraction_trna_charged across elongation_model values, and never read a within-family spread from steady_state rows as evidence about isoacceptors. Two runs of one design under different elongation models are separate experiments — they carry different design tags, different run paths and different dedup keys, and are not replicates of each other. ppgpp_conc needs the same care: only steady_state runs synthesise or degrade ppGpp, so a flat ppGpp trace under a kinetic model is a missing mechanism rather than a failed stringent response.

Degradation rates: 854 of 3,133 mRNA units carry a value that is not a fit

Every run in this corpus shares ONE fitted parameter set, produced by the model's parameter calculator (ParCa). For mRNA degradation, that calculator solves a non-negative least squares over the cistron x transcription-unit matrix under a lower bound on the rate — and for a large minority of units it does not return a fitted value at all. Measured on the knowledge base behind most of this corpus (kb_sha256 = 3b2f8ebd…):

class	units	what the number actually is
floor	245	the rate FLOOR — the slowest single measured mRNA cistron in the organism, applied as a lower bound. The solution hit the wall and stopped there
ceiling	7	the rate CEILING — the fastest single measured cistron, applied as an upper bound
imputed	602	the MEAN of the reported half-lives. These units' cistrons were never measured, so they carry a population default
(determined)	2,279	genuinely inferred from data

854 units, 27.3% of mRNA units, carrying 12.087% of mRNA expression in the basal condition (11.165%–15.491% across 67 conditions). On disk all four classes are the same float in the same array — nothing in sim_data distinguishes a fitted rate from a bound or a default.

Why this reaches you even if you never ask about half-lives. A transcript's degradation rate sets its steady-state level, which sets translation, which sets protein copy number. The two most-expressed not-a-fit units are RIBOSOMAL PROTEIN operons — rpmJ (1.584% of mRNA expression) and rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO (1.582%), both on the floor. Any statement about ribosomal protein abundance in this corpus rests on a parameter that was bounded rather than measured.

The index ships with the corpus

parca/deg_rate_baseline.json — the 854 unit ids with per-unit expression weights, frozen against the kb_sha256 above. parca/deg_rate_aliases.json — the same set joined into GENE space (1,149 genes, 4,557 aliases: symbols, b-numbers/EcoCyc ids, cistron ids, monomer ids), so you can check a gene without resolving transcription units yourself.

import json
alias = json.load(open("parca/deg_rate_aliases.json"))
g = alias["alias"].get("rple")                      # any symbol, cistron id or monomer id, lowercased
print(alias["genes"][g])
# {'sym': 'rplE', 'cls': ['floor'], 'pct': 1.581586,
#  'units': ['rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO[c]']}

pct is the share of TOTAL mRNA expression held by the not-a-fit units that gene belongs to. These weights do not sum: operon co-members each carry the operon's full share, so adding them across genes double-counts. The corpus figure is 12.087%.

Scope. The classification was measured on one knowledge base. It covers 279 of the 363 manifest rows; the other two arms were fitted separately and the same unit may fall in a different class there. Check kb_sha256 on the row before applying it.

Get a run's full trajectory

hf download evanniko1/cellarium-corpus --repo-type dataset \
  --include 'runs/cellarium/gene_knockout_001594/000000.tar.gz' --local-dir .
tar xzf runs/cellarium/gene_knockout_001594/000000.tar.gz

Provenance, license & citation

The software that produced this data is the Covert Lab wcEcoli whole-cell model, licensed under the Stanford Academic Software License Agreement (Docket S18-475) — non-commercial academic use. This dataset contains derived simulation output, shared for non-commercial academic research with attribution; it is not the wcEcoli software and confers no rights to it. Users of the underlying model must obtain and accept its license separately. If you are the rights holder and have concerns, please open a discussion.

Please cite the wcEcoli model (Macklin et al., Science 2020) and this dataset. QC-flagged rows (qc != "ok", including crashed lethal KOs and empty reads) are kept on purpose as first-class negative results — do not treat them as noise.

Generated with the Cellarium platform.