cSynBioSys/well4cell

The Well for The Cell

Version 1.0.0-rc2, built 2026-11-04T21:35:41+00:00 by the well4cell builder at wcEcoli commit 622a29c81d6785af8b5d81c4bcf8a500204a951b. That is the code that built this repo, not a simulator commit; the simulations ran under the commits in index.git_hash (see Provenance), and manifest.json lists both (builder_commit, simulator_commits).

Time series from the wcEcoli whole-cell model of Escherichia coli. Each sample is one cell generation: the cell from birth to division (or to the step at which the simulation stopped), recorded every 1 s of simulated time. Lineages are simulated for several generations, and the samples of one lineage are linked by parent_id. The 139,039 trajectories come from 36,828 lineages of 4,618 distinct cells (design x condition), grouped into five families by campaign tier.

family	tier	what varies	cells	lineages	trajectories
wildtype_media	T1	wild-type cells in a range of static media	41	328	1,281
single_knockout	T2	single-gene knockouts across media	3,206	25,544	97,478
dynamic_media	T3	media shifts and sinusoidal media schedules	776	6,197	21,404
regulation	T4	transcription-factor activity and ppGpp set-point perturbations	64	512	2,046
double_knockout	T5	two-gene knockouts	531	4,247	16,830
total			4,618	36,828	139,039

Limitations

Read this before using the data. Every number below is computed from this release's index unless it says it was measured on 1.0.0-rc1; each limitation has an index column, so nothing needs a side table. Rows are flagged, never removed: filter with the columns named.

1. Partial knockouts. A knockout zeroes whole transcription units (TUs), and the campaign mapped each gene to one TU. A gene that sits in several TUs kept transcribing from the others: 1,145 knockout cells, 35,552 trajectories (770 single, 180 media-shift and 195 double-knockout cells), confirmed on protein counts (lpxD, ispH and pgk stay at wild-type level in all four generations). Columns: partial_knockout, knockout_target_tus_missing; these rows are superseded. 1.0.0-rc2 re-ran them over every TU of every target (multi_gene_knockout, cell_id suffix @rc2, 21,097 trajectories in 698 re-run cells) and superseded_reason says what replaced each: rerun, its own re-run, 698 cells (22,245 trajectories); duplicate, the re-run of the identical design, because its own would have been a bit-identical copy (operon mates now zero the same units; glc_* labels run as basal), 319 cells (10,058 trajectories); placeholder, not re-run because the design switches into a placeholder medium (7), 60 cells (1,073 trajectories); not_replaced, re-run missing, 68 cells (2,176 trajectories). superseded_by names the replacing cell for rerun and duplicate.
2. Collateral genes. Of the 2,436 single knockouts that did silence their target, 1,276 also fully silence at least one other gene and 1,523 take at least one TU from another gene (up to 11 genes fully silenced: T2/wzyE_KO/acetate also silences rffC, rffG, rffH, rffM, wecA, wecB, wecC, wecE, wecF, wzxE, wzzE). A cell labelled X_KO is a knockout of X's TU, an operon knockout. Columns: collateral_genes_full, collateral_genes_partial.
3. Duplicate designs. Genes that share a TU give the same simulation: 369 single-knockout groups (918 cells) and 82 dynamic_media groups (212 cells) have the same zeroed TUs and the same condition label, and same-seed copies are bit-identical (447 pairs, 13,108 trajectories compared byte for byte on rc1; the rest are flagged by design identity). With the glucose doses folded (4) the 2,217 single-knockout designs cover 3,206 cells. Columns: design_id, and canonical on one cell per design (102,362 trajectories). 43 multi-cell designs mix parameter sets or simulator commits: those cells are the same design, not bit-identical twins.
4. Splits. 1.0.0-rc1's split_by_lineage was stratified by cell, so bit-identical twins sat on both sides (977 to 3,135 twin lineage pairs, depending on how the pairs are counted), and split_by_gene held out gene symbols rather than TUs (160 of 2,578 groups leaked, 18,502 trajectories). Both splits are now on designs: split_by_lineage assigns a design's seed as one unit and split_by_tu holds out TUs, so no twin crosses a split. split_by_gene is gone; its values remain at Hub revision 1.0.0-rc1.
5. Glucose doses. basal, glc_20mM, glc_5mM and glc_2mM are the same cell: glucose uptake is a switch, not a saturable rate, so the dose has nothing to act on (knockout in glc_20mM equals basal in 16,498 of 16,498 trajectories compared on rc1). condition_effective folds them into basal (19,364 rows). It also replaces the label of regulation cells, whose campaign condition the simulator ignores (e.g. T4/bglJ/active and T4/cytR/active, labelled acetate and succinate, ran in minimal): 19,747 rows in all have condition_effective different from condition. The 384 sinusoidal-media trajectories have none (a continuous mixture; read media_a/media_b); the glucose sinusoid is probably static basal for the same reason, but that was not checked.
6. Shifts, not adapted cells. No wild-type or knockout run set an initial condition, so every one started from the cell fitted to basal (medium_fitted_for minimal) and a static medium is a switch at t = 0 (shift_at_t0, 76,935 trajectories). Every such lineage is a shift experiment, not an adapted cell (unfitted_shift t0, 76,935 trajectories in 2,490 cells): expression stays fitted to basal while replication initiation follows the new medium. In a carbon source generation 0 over-initiates and generations 1 and 2 divide early (acetate birth dry mass 354, 202, 146 fg in generations 0 to 2 on rc1); in with_aa (28,108 trajectories) generation 0 divides at the basal time (about 2,800 s) where a cell fitted to with_aa takes about 1,400 s (measured on rc1). The adapted range arrives only after this campaign's four generations. Cells fitted to their medium (ppgpp_conc, tf_activity, the amino-acid shift controls) are not shifts. A later switch into a medium the cell is not fitted for (unfitted_shift mid_run, 13,633 trajectories in 436 cells; placeholder media are withdrawn instead, 7) does the same after the switch: the 177 trajectories that divide one second after birth are all of this kind (dynamic_media, 0 minimal, 1200 minimal_acetate, generation 2), not static acetate cells.
7. Placeholder media. minimal_minus_phosphate and minimal_no_glucose were added to the campaign as placeholders with invented doubling times; the model has no starvation response (on rc1, protein synthesis continued unchanged until ATP ran out). 418 trajectories are born into minimal_minus_phosphate (0 divide) and 1,547 into minimal_no_glucose (898 divide). withdrawn marks every generation in which one is in effect: 3,565 trajectories in 200 cells, with withdrawn_reason.
8. Divided is not viable. Division follows replication, not translation, so a cell can divide with its ribosomes stopped: 9,093 trajectories have translation_collapse, 6,264 of them divided, and in some lineages protein at birth halves every generation. 185 trajectories have 10 steps or fewer (short_trajectory), 177 of them divided (the one-second divisions of 6). viable = divided, not translation_collapse and not short_trajectory: 126,983 viable, 12,056 not.
9. tRNA charging channels only from rc2 runs. aa_pool_size, ntp_pool_size, trna_charged_fraction were dropped between the simulation and the export for every run converted before rc2, and the raw output they could be recomputed from was pruned: 117,174 trajectories have trna_channels false. The 21,865 trajectories with trna_channels true recorded them (per amino acid / per NTP). They are in the charging config.
10. Knockout versus wild type crosses parameter sets and code. Single knockouts: 83,937 on 8ff93a58 / c47683e1, 12,937 on 8ff93a58 / 0bb320c6, 360 on 8ff93a58 / 2760c49a, 244 on 8ff93a58 / 2ddbcd27. Wild type: 604 on b1750cf0 / c41efd75, 512 on 8ff93a58 / ba6ff555, 128 on b1750cf0 / ba6ff555, 29 on 8ff93a58 / ddc88250, 4 on b1750cf0 / e319d09f, 4 on b1750cf0 / 18a908d2. Double knockouts: 11,776 on b1750cf0 / c41efd75, 2,074 on 8ff93a58 / ba6ff555, 1,468 on 8ff93a58 / 0bb320c6, 1,185 on 8ff93a58 / c5f0fa9e, 152 on 8ff93a58 / 851724c1, 103 on 8ff93a58 / c462ae99, 58 on 8ff93a58 / c47683e1, 14 on 8ff93a58 / ddc88250. So the release's most obvious comparison, knockout against wild type, also compares two parameter sets (they differ by 11 keys added for the cytR fix, no changed values) and two code versions (the knockout commit changed amino-acid synthesis, FBA retries, equilibrium and lineage termination). Compare only rows with equal kb_sha256 and git_hash; 1.0.0-rc2 adds wild-type controls run with the re-runs' code (24 cells, 768 trajectories, cell_id suffix @rc2 on 8ff93a58 (640 trajectories), b1750cf0 (128 trajectories)): pair each rc2 knockout with the rc2 wild type of the same condition, kb_sha256 and git_hash.
11. Off-union flux: 8 trajectories withdrawn from metabolism and metabolism_1s. Matrix columns are frozen at the active union of 1.0.0-rc1 (the published rc1 parts cannot be rebuilt, so a reaction no rc1 trajectory used has no column). The export zeroes off-union values below 1e-06 as solver noise (counted in provenance/export_qc.parquet, offunion_zeroed). A trajectory with real flux there is not published in the configs that carry that matrix, because dropping the flux would publish a wrong matrix: column withdrawn_configs, reason offunion_flux in withdrawn_configs_reason. Withdrawn from metabolism and metabolism_1s: 8 trajectories of the rc2 re-runs, in 3 cells; all their other configs are published, and they are not withdrawn.
    • T2/trpS_KO/with_aa@rc2: 6 of its 31 trajectories (s0/g0, s2/g0, s4/g0, s5/g0, s6/g0, s7/g0); TRANS-RXN-312 (phenylalanine ABC uptake) in 6, ABC-15-RXN (isoleucine ABC uptake) in 1, ABC-2-RXN-ATP/ARABINOSE/WATER//ADP/CPD-15699/Pi/PROTON.45. (arabinose ABC uptake) in 1, ABC-35-RXN (leucine ABC uptake) in 1, TRANS-RXN-2 (Kdp potassium uptake) in 1; max flux 0.0255 to 0.295 at t = 2,099-3,008 s. The rc2 re-run silences every transcription unit of trpS (tryptophanyl-tRNA synthetase); rc1's T2/trpS_KO/with_aa was a partial knockout (1) that kept trpS expressed and never used these reactions, so the full knockout activates fluxes that are not in the frozen union.
    • T2/atpA_KO/with_aa@rc2: 1 of its 32 trajectories (s5/g0); TRANS-RXN-40-CPD-15699/PROTON//CPD-15699/PROTON.35. (YdeA arabinose export); max flux 8.08 at t = 2,734-2,751 s.
    • T2/rplT_KO/basal@rc2: 1 of its 10 trajectories (s4/g3); TRANS-RXN0-570 (pyruvate export to the periplasm); max flux 1 at t = 216 s.

What that leaves. The knockout rows (132,926 trajectories, 4,425 cells), each counted at its first step, in the order of the 1.0.0-rc1 review:

step	trajectories	cells	review (rc1)
the knockout did not happen (superseded): replaced by a re-run or not re-run	35,552	1,145	35,552 / 1,145
a twin of another cell with the same label (operon mates; not canonical)	12,690	435	12,562 / 431
a glucose-dose copy of a basal design (not canonical)	10,723	360	10,723 / 360
t = 0 switch into a medium the cell is not fitted for (unfitted_shift t0; the review: carbon sources only): a shift experiment	49,492	1,618	22,007 / 722
mid-run switch into a medium the cell is not fitted for (unfitted_shift mid_run; the review: acetate or no oxygen only): a shift experiment	7,394	240	3,539 / 116
placeholder medium (withdrawn)	1,998	112	2,030 / 116
usable: target silenced, no duplicate, no switch into a medium the cell is not fitted for, no placeholder medium	15,077	515	25,416 / 837

Partition: usable 15,077, relabel as shift experiments 56,886, redundant copies 23,413, re-run 35,552, withdraw 1,998. The flags differ from the review in two ways. Every switch into a medium the cell is not fitted for is a shift, not only carbon sources and anoxia: static with_aa (18,244 trajectories) and mid-run switches into with_aa move from usable to relabel, so every usable row is basal. And withdrawn is per generation: a lineage's first generations that divided before the switch into a placeholder are not withdrawn (cells are counted in every step one of their rows reaches). Even usable rows need the collateral genes read (308 cells, 8,951 trajectories touch another gene) and the viability filter (13,691 of 15,077 are viable).

Selecting rows

Every row of every release stays in the index; the flags say what each one is. To study knockouts with one row per experiment, in a medium the cell was fitted for:

import pandas as pd

index = pd.read_parquet("hf://datasets/cSynBioSys/well4cell/index.parquet")
usable = index[~index.superseded & ~index.withdrawn & index.canonical
               & index.unfitted_shift.isna() & index.viable.eq(True)]

• superseded: drop. The row's knockout did not silence its target; superseded_by names the cell that replaces it (superseded_reason rerun or duplicate), and index[index.cell_id == row.superseded_by] are the replacement's rows.
• withdrawn: drop: a placeholder medium with no mechanism in the model.
• canonical: keep to count each design once (operon mates and glucose-dose labels are one design).
• unfitted_shift: null for a cell in the medium it was fitted for; t0/mid_run rows are shift experiments, not adapted cells (keep them only for that).
• viable: divided, no translation collapse, not a 10-step trajectory; use it rather than divided.
• Controls: compare a knockout only with wild-type rows of equal kb_sha256 and git_hash (10).
• withdrawn_configs: 8 trajectories are missing from some configs on purpose (metabolism 8, metabolism_1s 8; offunion_flux: real flux in a reaction outside the published columns, limitation 11). Their other configs are published; their locators in the withdrawn configs are null.
• The rc2 re-runs (21,865 trajectories in 722 cells: 21,097 knockout trajectories, 768 wild-type) are the rows whose cell_id ends in @rc2 or @rc2-b1750cf0; they are the only rows in the charging config (trna_channels).

What is in this repo

Which families of each config are uploaded here (size on the Hub):

family	trajectories	summary	core	expression	metabolism	expression_1s	metabolism_1s	charging
wildtype_media	1,281	yes (325.5 KB)	yes (205.0 MB)	yes (1.0 GB)	yes (996.9 MB)	yes (4.0 GB)	yes (9.7 GB)	yes (267.4 MB)
single_knockout	97,478	yes (29.1 MB)	yes (15.8 GB)	yes (68.6 GB)	yes (76.5 GB)	yes (272.3 GB)	yes (746.2 GB)	yes (5.4 GB)
dynamic_media	21,404	yes (7.5 MB)	yes (3.3 GB)	yes (13.5 GB)	yes (15.8 GB)	yes (53.4 GB)	yes (154.2 GB)	yes (1.2 GB)
regulation	2,046	yes (736.0 KB)	yes (323.9 MB)	yes (1.7 GB)	yes (1.6 GB)	yes (6.5 GB)	yes (15.6 GB)	no rows
double_knockout	16,830	yes (5.9 MB)	yes (2.6 GB)	yes (12.2 GB)	yes (12.7 GB)	yes (48.5 GB)	yes (123.7 GB)	yes (1.9 GB)

Every config is complete: all five families are in this repo.

index.parquet lists every trajectory, uploaded or not. Its locator columns (<config>_file, <config>_row_offset, <config>_n_rows) are null for data not in this repo, so index["<config>_file"].notnull() (e.g. index.expression_file.notnull()) is the authoritative availability check. load_dataset(..., "<config>", split="<family>") fails for a family that has not been uploaded (e.g. load_dataset(..., "expression", split="single_knockout") until that family is uploaded).

Configs

Each config is one data product. summary is one row per trajectory and joins to index.parquet on sample_id: n_steps and, for each of the 18 scalar channels in the order of the product schema, <channel>_mean, _min, _max, _first and _last over the trajectory's 1 s core rows (int32 for mrna_counts and n_oric except _mean, float32 otherwise; the growth_rate statistics skip its null row 0, so growth_rate_first is the value at t = 1). For every family it also has 13 pathway proteome fractions, pathway_translation_ribosome, pathway_transcription_rnap, pathway_stringent_response, pathway_glycolysis, pathway_tca_cycle, pathway_pentose_phosphate, pathway_respiration_atp, pathway_aa_biosynthesis, pathway_amr_efflux, pathway_oxidative_stress, pathway_global_regulators, pathway_proteostasis and pathway_cell_division (float32, unit fraction): for each pathway of the Cellarium pathway panel, the pathway's protein counts over all protein counts at each 10 s expression row, averaged over the trajectory (Cellarium's definition; the gene lists are in Cellarium's pathway_panel.py). Every other config but charging (see tRNA charging) carries sample_id, t, t_abs and the 18 scalar channels; the matrix configs add per-gene or per-reaction columns. expression and metabolism keep the rows with t % 10 == 0 plus each trajectory's last row (point samples, not averages); expression_1s and metabolism_1s keep every row. The split of every config is the family. expression and metabolism are exact row subsets of expression_1s and metabolism_1s; they are kept for loader compatibility and will be reconsidered at 1.0.0.

config	rows every	matrices (active columns)	trajectories	rows	size
summary	trajectory	none: n_steps and _mean, _min, _max, _first, _last of each scalar; 13 pathway_<name> fractions	139,039	139,039	43.6 MB
core	1 s	scalars only	139,039	379,148,262	22.2 GB
expression	10 s	mrna_counts_matrix (2,773), protein_counts_matrix (4,174)	139,039	38,098,821	97.1 GB
metabolism	10 s	reaction_flux_matrix (3,974), exchange_flux_matrix (82)	139,031	38,096,827	107.6 GB
expression_1s	1 s	mrna_counts_matrix (2,773), protein_counts_matrix (4,174)	139,039	379,148,262	384.7 GB
metabolism_1s	1 s	reaction_flux_matrix (3,974), exchange_flux_matrix (82)	139,031	379,128,423	1.0 TB
charging	1 s	aa_pool_size (21), ntp_pool_size (4), trna_charged_fraction (21)	21,865 (wildtype_media, single_knockout, dynamic_media, double_knockout only)	62,396,417	8.8 GB

Matrix columns are pruned to the columns that are non-zero at least once anywhere in the campaign (active columns: mrna_counts 2,773 of 3,133, protein_counts 4,174 of 4,310, reaction_flux 3,974 of 9,612, exchange_flux 82 of 87). The full column lists, with an active mask and each active column's position in the product (product_column), are in provenance/reference/<matrix>.parquet.

tRNA charging

The charging config has one row per 1 s step, like core, but no scalars: sample_id, t, t_abs, aa_pool_size (fixed_size_list[21], molecules), ntp_pool_size ([4], molecules) and trna_charged_fraction ([21], fraction of each amino acid's tRNAs that is charged). Join it to core on (sample_id, t). Column k of a list is the row with column == k of provenance/reference/charging_<column>.parquet (21 amino acids, ATP/CTP/GTP/UTP). It holds only trajectories with index trna_channels true: runs converted from rc2 on (21,865 trajectories); every rc1 row has none, and never will (their raw output is deleted). Coverage: 21,865 trajectories in this release (62,396,417 rows). Row 0 (t = 0) of every list is NaN: the simulator's listener writes an all-zero first row before its first step (checked at export), like growth_rate, which is null there.

index.parquet

One row per trajectory, sorted by family (tier order T1..T5), cell_id, seed, generation.

column	type	meaning
sample_id	string	trajectory id, lineage_id + "/g{generation}"
lineage_id	string	cell_id + "/s{seed}": one simulated lineage
cell_id	string	the experimental cell (design x condition), e.g. T2/argG_KO/basal; see Ids
parent_id	string	sample_id of the mother generation; null at generation 0
experiment_name	string	the campaign's experiment name, verbatim (wrong for T4 transcription-factor cells; see Ids)
family	string	one of the five families (the split names of every data config)
tier	string	campaign tier, T1..T5
variant_type	string	wcEcoli variant name
variant_index	int32	wcEcoli variant index
variant	string	gene symbol(s), wildtype, or the variant type
condition	string	the campaign's condition as designed; ignored by the simulator for TF-activity and sinusoidal cells (read media_schedule)
timeline	string	the media schedule that actually ran, "0 minimal, 1200 minimal_acetate" (simulation seconds); null for sinusoidal media
seed	int8	simulation seed
generation	int8	generation number within the lineage (0 = first cell)
knockout_genes	list<element: string>	knocked-out gene symbols
knockout_gene_ids	list<element: string>	knocked-out gene ids (EcoCyc)
knockout_tu_ids	list<element: string>	transcription units whose expression was set to zero (a knockout removes a whole TU)
media_schedule	list<element: struct<t_abs_sec: int32, medium: string>>	media changes, lineage-absolute seconds (t_abs_sec) and medium
medium_at_birth	string	medium at the first row of this generation
medium_at_division	string	medium at the last row of this generation
media_a	string	first medium of a two-medium schedule
media_b	string	second medium of a two-medium schedule
period_sec	int32	period of a sinusoidal schedule, s (null otherwise)
tf_target	string	symbol of the transcription factor that was actually perturbed (regulation family)
tf_target_id	string	EcoCyc id of that transcription factor
tf_state	string	imposed TF state: active, inactive, or control
ppgpp_setpoint_um	float	ppGpp set point, uM (regulation family)
ppgpp_factor	float	multiple of the basal ppGpp concentration (0.2..2.0)
aa_shift	string	amino-acid shift label, e.g. +ARG, -ARG, rich->6aa, control
perturbation_text	string	one-sentence plain-language description of the perturbation
n_steps	int32	rows of this trajectory at 1 s
divided	bool	the cell divided (= not terminated)
terminated	bool	the lineage ended in this generation
termination_class	string	none, time_limit, negative_counts, fba_infeasible, equilibrium_unstable, other
translation_collapse	bool	Cellarium's translation collapse, ribosome_elongation_rate_mean < 1 (aa/s) in the summary config; null for a trajectory without a summary row (see Outcomes)
termination_reason	string	the simulator's termination message
trna_channels	bool	the run's raw output recorded aa_pool_size, ntp_pool_size and trna_charged_fraction (false for every run converted before rc2; see Provenance)
division_time_sec	float	n_steps - 1 when divided, else null
final_mass_fg	float	cell mass at the last row, fg
growth_rate	float	mean instantaneous growth rate over the generation, 1/s
lineage_terminated	bool	the lineage ended in some generation
lineage_generations	int8	generations present for this lineage
condition_effective	string	the condition that actually ran: the campaign condition of the medium at t = 0, with glc_20mM/glc_5mM/glc_2mM folded into basal; null for sinusoidal media (see Limitations)
medium_fitted_for	string	medium of the condition the first cell was initialised (fitted) from; minimal for every wild-type and knockout cell whatever its label
shift_at_t0	bool	the medium at t = 0 is not medium_fitted_for: a cell fitted to one medium switched into another at t = 0 (null for sinusoidal media)
unfitted_shift	string	t0 (= shift_at_t0) or mid_run (a later switch into a medium other than medium_fitted_for, glucose doses as minimal, placeholders excepted) when the cell meets a medium its expression was not fitted for; a shift experiment, not an adapted cell
partial_knockout	bool	a targeted gene kept a transcription unit: the knockout did not silence it
knockout_target_tus_missing	list<element: string>	transcription units of the targeted genes that were not zeroed (null without a knockout)
collateral_genes_full	list<element: string>	other genes every transcription unit of which was zeroed (silenced with the target)
collateral_genes_partial	list<element: string>	other genes that lost some but not all of their transcription units
superseded	bool	replaced by a re-run (every partial knockout); kept for the record
superseded_by	string	cell_id of the re-run that replaces this cell: its own re-run, or for a duplicate the re-run of the identical design (null when nothing replaces it)
superseded_reason	string	rerun (replaced by its own re-run), duplicate (not re-run: its re-run would be a bit-identical copy of another cell's, an operon mate or a glucose-dose label; superseded_by names that re-run), placeholder (not re-run: the design switches into a placeholder medium), not_replaced (its re-run is missing), pending (no re-run published yet); null when not superseded
withdrawn	bool	a placeholder medium with no mechanism in the model is in effect in this generation
withdrawn_reason	string	why the row is withdrawn
design_id	string	hash of everything the simulator was given (zeroed TUs, fitted-for medium, schedule with glucose doses folded, sinusoid, TF state, ppGpp factor, amino-acid shift); twins share it
canonical	bool	true on one cell per design (keep canonical rows to count each experiment once)
short_trajectory	bool	n_steps <= 10
viable	bool	divided, not translation_collapse and not short_trajectory; null when that depends on a null translation_collapse
split_by_lineage	string	train/val/test over a design's seeds: every lineage of every cell of a design with one seed is in one split, so twins never cross
split_by_tu	string	train/val/test holding out whole transcription units; a row takes the most held-out split of its knockout_tu_ids; non-knockout rows are train
withdrawn_configs	list<element: string>	configs this trajectory is not published in, though the row is otherwise usable (empty for almost every row): offunion_flux withdraws metabolism and metabolism_1s of a trajectory with real flux in a reaction outside the published active columns
withdrawn_configs_reason	string	why withdrawn_configs is set: offunion_flux: <matrix, reaction, max flux, rows>; null when it is empty
job_id	int32	campaign job id
attempt	int8	campaign job attempt
started_at	string	simulation start time
run_dir	string	campaign run directory
h5_group	string	group in the run's channels.h5, e.g. seed0/gen0
git_hash	string	wcEcoli commit that ran the simulation
parca_cache	string	Parca (fitted-parameter) cache the run used, by name; the cache itself is not distributed
kb_sha256	string	sha256 of the fitted parameter set (simData.cPickle) used; the set itself is not distributed
sim_options_hash	string	sha256 of the run's simulation options minus per-run keys and the keys carried as columns (git_hash, timeline, multi-knockout indices); key into provenance/sim_options/
<config>_file, <config>_row_offset, <config>_n_rows	string, int64, int32	locator of this trajectory in each config: file path in the repo, first row, row count (null when the trajectory is not in that config)

Product schema

Rows of one trajectory are contiguous and in time order within one file. Units are also in each field's parquet metadata (unit).

column	type	unit	meaning
sample_id	dictionary<values=string, indices=int32, ordered=0>		joins to index.parquet
t	int32	s	seconds since this cell's birth; row 0 is the birth state
t_abs	int32	s	seconds since the lineage began (continues across generations)
cell_mass	float	fg	total cell mass
dry_mass	float	fg	dry mass
protein_mass	float	fg	protein mass
rna_mass	float	fg	RNA mass
dna_mass	float	fg	DNA mass
small_molecule_mass	float	fg	small-molecule mass
cell_volume	float	fL	cell volume
growth_rate	float	1/s	instantaneous growth rate (null at row 0)
ppgpp_conc	float	uM	ppGpp concentration
aa_supply_total	float	counts/s	total amino-acid supply rate
aa_synthesis_total	float	counts/s	total amino-acid synthesis rate
mrna_counts	int32	molecules	total mRNA molecules
n_oric	int32	count	origins of replication
fba_objective	float	mmol/gDCW/h	FBA objective value
exchange_flux_total	float	mmol/gDCW/h	sum of exchange fluxes
reaction_flux_total	float	mmol/gDCW/h	sum of reaction fluxes
ribosome_elongation_rate	float	aa/s	ribosome elongation rate
ribosome_actual_elongations	float	aa	amino acids elongated in the step
mrna_counts_matrix	fixed_size_list<element: int32 not null>[2773]	molecules	mRNA counts per transcription unit (ids are mRNA TU ids); column k is the row of provenance/reference/mrna_counts.parquet with product_column == k
protein_counts_matrix	fixed_size_list<element: int32 not null>[4174]	molecules	protein counts per monomer; column k is the row of provenance/reference/protein_counts.parquet with product_column == k
reaction_flux_matrix	fixed_size_list<element: float not null>[3974]	mmol/gDCW/h	flux per metabolic reaction; column k is the row of provenance/reference/reaction_flux.parquet with product_column == k
exchange_flux_matrix	fixed_size_list<element: float not null>[82]	mmol/gDCW/h	flux per exchange reaction; column k is the row of provenance/reference/exchange_flux.parquet with product_column == k

Loading

from datasets import load_dataset

index = load_dataset("cSynBioSys/well4cell", "index", split="train")
core = load_dataset("cSynBioSys/well4cell", "core", split="single_knockout", streaming=True)
expression = load_dataset("cSynBioSys/well4cell", "expression", split="wildtype_media")

DuckDB, one trajectory:

SELECT t, cell_mass, growth_rate
FROM 'hf://datasets/cSynBioSys/well4cell/data/core/*/*.parquet'
WHERE sample_id = 'T1/WT/acetate/s0/g0'
ORDER BY t;

One trajectory by its locator (reads only the row groups it spans):

import pyarrow.parquet as pq
from huggingface_hub import hf_hub_download

row = index.filter(lambda r: r["sample_id"] == "T1/WT/acetate/s0/g0")[0]
path = hf_hub_download("cSynBioSys/well4cell", row["expression_file"], repo_type="dataset")
table = pq.read_table(path, filters=[("sample_id", "=", row["sample_id"])])
assert table.num_rows == row["expression_n_rows"]

Ids

• cell_id is the campaign experiment name, slugified, with the tier as a plain T1..T5 prefix: [T2_CORE] argG_KO/basal becomes T2/argG_KO/basal. The raw name is in experiment_name.
• Regulation (T4) transcription-factor cells are the exception: the campaign named them from the sorted TF symbols while the simulator indexes the sorted TF ids, so their experiment names name the wrong TF ([T4] araC/active ran trpR). Their cell_id, tf_target and tf_target_id use the TF that actually ran (T4/trpR/active); experiment_name keeps the campaign's name.
• A knockout removes a whole transcription unit: the model sets the expression of one TU to zero, so other genes of that TU are silenced too. knockout_genes lists the targeted genes, knockout_tu_ids the TUs actually knocked out.
• lineage_id = cell_id + "/s{seed}"; sample_id = lineage_id + "/g{generation}", e.g. T1/WT/acetate/s0/g0.
• parent_id is the previous generation's sample_id (null at generation 0).

Time axis

• Steps are 1 s. t restarts at 0 for every generation; t_abs continues across the generations of a lineage, so generation g+1 starts where generation g ended.
• Row 0 is the birth state: the daughter at half the mother's mass. growth_rate is null at row 0 (no step has been taken yet).
• Only one daughter is followed at each division, so a lineage is a chain, not a tree.
• A generation stopped by the per-generation time limit (TimeLimitReached) has 10,801 steps (0..10,800 s).

Outcomes

divided is true when the cell divided. terminated marks the generation in which the lineage ended, and termination_class says why:

termination_class	meaning	trajectories
none	divided normally	133,423
time_limit	reached the time limit without dividing: the only clean non-division (slow or arrested growth)	2,655
negative_counts	a molecule count went negative (numerical failure)	2,949
fba_infeasible	the metabolism FBA problem had no solution	4
equilibrium_unstable	the equilibrium solver failed	8
other	any other simulator exception	0

time_limit is the only clean non-division; the other classes are solver failures, and the rows before the failure are kept as recorded.

The same outcomes in the qc vocabulary of the Cellarium corpus:

well4cell termination_class	Cellarium qc	meaning
none	ok	the cell divided
time_limit	no_division	the generation ran to the time limit without dividing; the model's "did not divide"
negative_counts	crashed	simulator error (a molecule count went negative)
fba_infeasible	fba_infeasible	metabolism solver failure
equilibrium_unstable	crashed	equilibrium solver failure
other	crashed	any other simulator error

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).

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). Here the flag is the index column translation_collapse, the same predicate as ribosome_elongation_rate_mean < 1 in the summary config (null for a trajectory without a summary row). It flags 9,093 trajectories in this release, 6,264 of them with termination_class none (divided, but with translation collapsed). Treat them as inviable in any viability task.

Suggested tasks

1. Growth-rate regression from the perturbation: predict growth_rate (index) from the perturbation columns (knockout_genes, media, tf_target, ...) and optionally the first rows of the trajectory.
2. Viability classification: predict whether a generation is not terminated by the time limit (termination_class != 'time_limit'), i.e. whether the perturbed cell still divides.
3. Forecasting: given the trajectory up to time t, predict the channels at t + h, with horizons h stated in seconds (e.g. 10, 60, 600 s) so 1 s and 10 s products compare directly.

Use split_by_lineage (train 111,233 / val 13,910 / test 13,896) to hold out whole replicate lineages of each design, or split_by_tu (train 107,228 / val 15,848 / test 15,963) to hold out whole transcription units; both are fixed columns of the index (seed 20261008) and both keep bit-identical twins on one side. For viability use viable, not divided; to count each experiment once keep canonical; leave out superseded and withdrawn rows (see Selecting rows).

Provenance

• Simulator commits (index.git_hash): 0bb320c6f684bab46b61109aff449848ada75fa9, 18a908d28303c2feeba161e962c049e4f712454e, 2760c49a91157e59184dd848bdfe2be9d17b0c07, 2ddbcd27be48e0ef25b762bbcff9f185eca70661, 5f5fa5f4fe2302af12385528d176f4d73c4bf3a6, 851724c1d520051ab5e9887136f8ad3c722c11e7, ba6ff555d3e566a9eb64490cfeb41f12e370d5ff, c41efd7561d40316e5e83b20e3fb27316845b0bc, c462ae99c47d24c327a0311edd785f664d8038bc, c47683e19614b17e9c022762a238a1b36aa12dd2, c5f0fa9e0aa1f36e323202cee5ace8fedcb9287b, ddc88250ad5c3ab07872c46888cd18f0fd3d32e6, e319d09f3749168155d246b103b7d37ba492ec63.
• Simulation options hashes (index.sim_options_hash): 2ba80aae18ba5904625753010432220257822ee442fe87c162cb651d35f5cc0f.
• Fitted parameters (index.parca_cache, with the sha256 of its simData.cPickle in index.kb_sha256): 5558948af4ad806f21d7c80c (sha256 8ff93a58576f484edfd6fea641eeeb4fc554b52b97da49f4d8b275ca74496667), fa6a9ebd4b1c988a36ef9fa1 (sha256 b1750cf04409c37ebce9d4d3009daeae0779dd66508812c2807744d83baf1ab7). The Parca caches themselves are not included in this repo (see Licence).
• Every trajectory ran with operons on and the steady-state tRNA charging model (trna_charging true, no kinetic charging), from one of two fitted parameter sets identified by kb_sha256 and parca_cache; do not pool rows across the two parameter sets without checking kb_sha256.
• provenance/scan_runs.parquet: every run directory read (37,992 runs), with its generation count and reference-id hash.
• provenance/failed_jobs.parquet: 1,164 campaign jobs that failed, with the error message and the generations they left behind.
• provenance/export_qc.parquet: the export checks of every trajectory in every config (717,104 trajectory x config writes checked, 60 failed): rows landed in the part file, steps are contiguous, counts are valid. A trajectory that fails is left out of that config. These checks say the rows were written correctly, not that the cell was healthy: the cells' outcomes are in termination_class, translation_collapse and viable (manifest.json: export_checks versus cell_health).
• stats/<family>.parquet: per product, channel and matrix column: mean, population std, min, max and row count.
• manifest.json: row and byte totals per config, counts per family.

Degradation rates. Not every mRNA half-life in the fitted parameters is a fit to that transcript. The fitted rates are bounded below by the slowest measured mRNA decay (the longest measured half-life), and a unit whose rate sits on that bound is on the floor. Rates faster than the fastest measured decay (the shortest measured half-life) are clipped to it, and those units are on the ceiling. A unit none of whose genes has a measured half-life is imputed: it carries the mean measured half-life. Any claim about the stability of these transcripts, or that depends on it, rests on a bound or a population mean, not on a measurement of that transcript. Which units are in each class is derived from the fitted parameters, so like them it is kept with the campaign and not distributed (see Licence). This repo has the counts only.

• 5558948af4ad806f21d7c80c: of 3,133 mRNA transcription units, 2,293 have a fitted rate and 840, carrying 12.2% of basal mRNA expression, do not: 246 on the floor, 7 on the ceiling and 587 imputed.
• fa6a9ebd4b1c988a36ef9fa1: of 3,133 mRNA transcription units, 2,293 have a fitted rate and 840, carrying 12.2% of basal mRNA expression, do not: 246 on the floor, 7 on the ceiling and 587 imputed.

Not recorded before rc2: aa_pool_size, ntp_pool_size, trna_charged_fraction (per amino acid / per NTP) were dropped by the exporter for runs converted before rc2; index trna_channels is false for 117,174 trajectories (those runs' raw output is deleted) and true for 21,865 whose runs recorded them. They are in the charging config.

Licence

CC BY 4.0 for everything in this repo. The wcEcoli model is by the Covert lab (Stanford) and is licensed separately under the Stanford Academic Software License; it is not included here. The fitted parameter sets (Parca caches) are not distributed either and are identified only by kb_sha256 / parca_cache, and the same applies to anything derived from them, such as the per-unit degradation-rate classification, of which only the counts are published (see Provenance); reproducing these simulations requires obtaining wcEcoli under its own licence.

Citation

@misc{well4cell,
  title  = {The Well for The Cell: whole-cell E. coli simulation trajectories},
  author = {Yermakov, Alexey},
  year   = {2026},
  url    = {https://huggingface.co/datasets/cSynBioSys/well4cell}
}

TODO(authors): the author list above is incomplete; it is completed before 1.0.0.