id stringlengths 19 46 | label stringlengths 17 68 | contributor stringclasses 1
value | host stringclasses 1
value | ts float64 1.78B 1.78B ⌀ | perturbation stringclasses 9
values | condition stringlengths 5 26 ⌀ | timeline stringclasses 2
values | seed int64 0 7 | generations int64 0 7 | qc stringclasses 6
values | generation_qc stringclasses 14
values | reportable bool 2
classes | note stringclasses 5
values | simout_path stringlengths 37 64 | channel_stats stringlengths 2 1.41k ⌀ | series stringlengths 2 5.08k ⌀ | media_segments stringlengths 2 866 ⌀ | growth_rate float64 0 0 ⌀ | cell_mass float64 404 198k ⌀ | dry_mass float64 121 81.4k ⌀ | protein_mass float64 14.9 503 ⌀ | rna_mass float64 8.58 207 ⌀ | ppgpp_conc float64 0 1.48k ⌀ | fba_objective float64 0.58 822 ⌀ | per_generation stringlengths 2 624 ⌀ | ribosome_conc float64 0 27.3 ⌀ | fraction_trna_charged float64 0 0.98 ⌀ | rela_conc float64 0 0.47 ⌀ | pathways stringlengths 2 533 ⌀ | division_rate float64 0 1 ⌀ | gens_reached int64 0 7 ⌀ | terminal_divided bool 2
classes | n_fba_failures int64 0 0 ⌀ | median_division_time_sec float64 1.26k 14.1k ⌀ | requested_generations int64 2 8 ⌀ | crashed bool 2
classes | species_panel stringlengths 2 75.9k ⌀ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
gene_knockout_2_a165bfd6 | gene_knockout·KO:rpoB·s2 | vmnik | vmsi | 1,783,804,790.820874 | gene_knockout | KO:rpoB | null | 2 | 0 | empty | ["empty"] | false | reader error: reader worker produced no JSON | runs/cellarium/gene_knockout_002095/000002 | {} | {} | [] | null | null | null | null | null | null | null | [] | null | null | null | {} | null | null | null | null | null | null | false | {} |
wildtype_2_8945e7db | wildtype·basal·s2 | vmnik | vmsi | 1,783,781,685.677321 | wildtype | basal | null | 2 | 6 | no_division | ["ok", "ok", "ok", "ok", "ok", "no_division"] | false | runs_armB_multiko/cellarium/wildtype_374656/000002 | {"growth_rate": {"mean": 0.00018702026028633077, "min": 0.00014188816971156206, "max": 0.0006119905483756244, "first": null, "last": 0.00017741372564802717}, "cell_mass": {"mean": 1148.07302705399, "min": 1043.4945741510533, "max": 1256.698353170219, "first": 1043.4945741510533, "last": 1256.698353170219}, "dry_mass": ... | {"growth_rate": [[15719.0, null], [15785.0, 0.00019012618672228793], [15851.0, 0.00017314340625841358], [15917.0, 0.0001903127432910813], [15984.0, 0.0001889072956980558], [16050.0, 0.0001835433201540076], [16116.0, 0.00019993123899582414], [16182.0, 0.0001914585280408389], [16248.0, 0.00019209054620667552], [16314.0, ... | [] | null | null | null | null | null | null | null | [{"i": 0, "growth": 0.00024060835142083233, "ppgpp": 64.10544897586627, "divided": true}, {"i": 1, "growth": 0.00023198380831246685, "ppgpp": 82.44959518623689, "divided": true}, {"i": 2, "growth": 0.00021730516431854534, "ppgpp": 78.28545473691479, "divided": true}, {"i": 3, "growth": 0.0002071064848171679, "ppgpp": 6... | null | null | null | {"translation_ribosome": 0.3312708059039473, "transcription_rnap": 0.003761098470429802, "stringent_response": 0.0014217056059293185, "glycolysis": 0.03442771377918641, "tca_cycle": 0.0159916552605661, "pentose_phosphate": 0.004690721177692188, "respiration_atp": 0.006489255958107658, "aa_biosynthesis": 0.0113795048375... | 0.833 | 6 | false | 0 | 9,200 | 8 | false | null | |
gene_knockout_0_88f56287 | gene_knockout·KO:rpoB·s0 | vmnik | vmsi | 1,783,781,699.668133 | gene_knockout | KO:rpoB | null | 0 | 6 | ok | ["ok", "ok", "ok", "ok", "ok", "ok"] | true | runs_armB_multiko/cellarium/gene_knockout_002095/000000 | {"cell_mass": {"mean": 1549.8927564306682, "min": 1215.615994141477, "max": 1932.5167151799371, "first": 1215.848221523739, "last": 1932.5167151799371}, "ppgpp_conc": {"mean": 51.30489049165967, "min": 0.0, "max": 57.07245042667536, "first": 0.0, "last": 55.93211964647455}, "fba_objective": {"mean": 1.306607128033303, ... | {"cell_mass": [[13161.0, 1215.848221523739], [13296.0, 1248.1790788600213], [13431.0, 1287.6795514693185], [13566.0, 1328.8986298908897], [13702.0, 1373.6046678237956], [13837.0, 1419.2370820511576], [13972.0, 1465.819600440422], [14107.0, 1513.935617357599], [14242.0, 1563.7706849429105], [14377.0, 1614.5237237078331]... | [{"media": "minimal", "t0": 13161.0, "t1": 15188.0, "n": 2028, "means": {"cell_mass": 1549.8927564306682, "ppgpp_conc": 51.30489049165967, "fba_objective": 1.306607128033303, "ribosome_conc": 20.483450085581005, "fraction_trna_charged": 0.9668949363218269, "rela_conc": 0.22432068386149093}}] | null | null | null | null | null | null | null | [{"i": 0, "growth": 0.00026825279077359875, "ppgpp": 51.26857572493178, "divided": true}, {"i": 1, "growth": 0.0002874785896517164, "ppgpp": 54.11385794412752, "divided": true}, {"i": 2, "growth": 0.00025942859264365884, "ppgpp": 70.44009732711913, "divided": true}, {"i": 3, "growth": 0.00022607658753626754, "ppgpp": 6... | null | null | null | {"translation_ribosome": 0.3534368861909903, "transcription_rnap": 0.0035895896439553134, "stringent_response": 0.0014814453982785988, "glycolysis": 0.03377415007852602, "tca_cycle": 0.01609441476817955, "pentose_phosphate": 0.004519096955772424, "respiration_atp": 0.007210620382538452, "aa_biosynthesis": 0.01293962883... | 1 | 6 | true | 0 | 8,975 | 8 | false | null | |
metabolism_kinetic_objective_weight_0_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1e-7_default seed0 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1e-7_default | null | 0 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000002/000000 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 2 | true | null |
metabolism_kinetic_objective_weight_0_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1e-8 seed0 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1e-8 | null | 0 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000001/000000 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 2 | true | null |
metabolism_kinetic_objective_weight_1_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1e-8 seed1 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1e-8 | null | 1 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000001/000001 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 2 | true | null |
metabolism_kinetic_objective_weight_1_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1e-7_default seed1 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1e-7_default | null | 1 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000002/000001 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 2 | true | null |
metabolism_kinetic_objective_weight_0_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1e-6 seed0 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1e-6 | null | 0 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000003/000000 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 2 | true | null |
metabolism_kinetic_objective_weight_1_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1e-6 seed1 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1e-6 | null | 1 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000003/000001 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 2 | true | null |
metabolism_kinetic_objective_weight_0_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1e-5 seed0 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1e-5 | null | 0 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000004/000000 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 2 | true | null |
metabolism_kinetic_objective_weight_1_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1e-5 seed1 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1e-5 | null | 1 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000004/000001 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 2 | true | null |
metabolism_secretion_penalty_0_crash | metabolism_secretion_penalty/minimal|sec_pen:5e-4 seed0 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:5e-4 | null | 0 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000003/000000 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 2 | true | null |
metabolism_secretion_penalty_1_crash | metabolism_secretion_penalty/minimal|sec_pen:5e-4 seed1 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:5e-4 | null | 1 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000003/000001 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 2 | true | null |
gene_knockout_0_3ccc7f83 | gene_knockout·KO:dnaN·s0 | vmnik | vmsi | 1,783,760,575.69026 | gene_knockout | KO:dnaN | null | 0 | 0 | crashed | ["ok"] | false | sim crashed: Command '['docker', 'run', '--rm', '-v', 'C:\\dev\\anthropic_hackathon\\runs:/wcEcoli/out', '-e', 'PYTHONPATH=/wcEcoli', '-w', '/wcEcoli', 'wcecoli-si | runs/cellarium/gene_knockout_000058/000000 | {} | {} | [] | null | null | null | null | null | null | null | [] | null | null | null | {} | null | null | null | null | null | 8 | true | null |
gene_knockout_2_9f75d194 | gene_knockout·KO:dnaN·s2 | vmnik | vmsi | 1,783,760,575.746006 | gene_knockout | KO:dnaN | null | 2 | 0 | crashed | ["ok"] | false | sim crashed: Command '['docker', 'run', '--rm', '-v', 'C:\\dev\\anthropic_hackathon\\runs:/wcEcoli/out', '-e', 'PYTHONPATH=/wcEcoli', '-w', '/wcEcoli', 'wcecoli-si | runs/cellarium/gene_knockout_000058/000002 | {} | {} | [] | null | null | null | null | null | null | null | [] | null | null | null | {} | null | null | null | null | null | 8 | true | null |
gene_knockout_1_47e01cea | gene_knockout·KO:dnaN·s1 | vmnik | vmsi | 1,783,760,575.766111 | gene_knockout | KO:dnaN | null | 1 | 0 | crashed | ["ok"] | false | sim crashed: Command '['docker', 'run', '--rm', '-v', 'C:\\dev\\anthropic_hackathon\\runs:/wcEcoli/out', '-e', 'PYTHONPATH=/wcEcoli', '-w', '/wcEcoli', 'wcecoli-si | runs/cellarium/gene_knockout_000058/000001 | {} | {} | [] | null | null | null | null | null | null | null | [] | null | null | null | {} | null | null | null | null | null | 8 | true | null |
gene_knockout_3_e68812f4 | gene_knockout·KO:dnaN·s3 | vmnik | vmsi | 1,783,760,575.78354 | gene_knockout | KO:dnaN | null | 3 | 0 | crashed | ["ok"] | false | sim crashed: Command '['docker', 'run', '--rm', '-v', 'C:\\dev\\anthropic_hackathon\\runs:/wcEcoli/out', '-e', 'PYTHONPATH=/wcEcoli', '-w', '/wcEcoli', 'wcecoli-si | runs/cellarium/gene_knockout_000058/000003 | {} | {} | [] | null | null | null | null | null | null | null | [] | null | null | null | {} | null | null | null | null | null | 8 | true | null |
condition_0_9286fc9c | condition·minus_phosphate·s0 | vmnik | vmsi | 1,783,760,575.800165 | condition | minus_phosphate | null | 0 | 0 | crashed | ["ok"] | false | sim crashed: Command '['docker', 'run', '--rm', '-v', 'C:\\dev\\anthropic_hackathon\\runs:/wcEcoli/out', '-e', 'PYTHONPATH=/wcEcoli', '-w', '/wcEcoli', 'wcecoli-si | runs/cellarium/condition_000012/000000 | {} | {} | [] | null | null | null | null | null | null | null | [] | null | null | null | {} | null | null | null | null | null | 8 | true | null |
condition_1_3f01d9c1 | condition·minus_phosphate·s1 | vmnik | vmsi | 1,783,760,575.816307 | condition | minus_phosphate | null | 1 | 0 | crashed | ["ok"] | false | sim crashed: Command '['docker', 'run', '--rm', '-v', 'C:\\dev\\anthropic_hackathon\\runs:/wcEcoli/out', '-e', 'PYTHONPATH=/wcEcoli', '-w', '/wcEcoli', 'wcecoli-si | runs/cellarium/condition_000012/000001 | {} | {} | [] | null | null | null | null | null | null | null | [] | null | null | null | {} | null | null | null | null | null | 8 | true | null |
condition_2_b0cb590c | condition·minus_phosphate·s2 | vmnik | vmsi | 1,783,760,575.831424 | condition | minus_phosphate | null | 2 | 0 | crashed | ["ok"] | false | sim crashed: Command '['docker', 'run', '--rm', '-v', 'C:\\dev\\anthropic_hackathon\\runs:/wcEcoli/out', '-e', 'PYTHONPATH=/wcEcoli', '-w', '/wcEcoli', 'wcecoli-si | runs/cellarium/condition_000012/000002 | {} | {} | [] | null | null | null | null | null | null | null | [] | null | null | null | {} | null | null | null | null | null | 8 | true | null |
condition_3_1b348ca3 | condition·minus_phosphate·s3 | vmnik | vmsi | 1,783,760,575.848178 | condition | minus_phosphate | null | 3 | 0 | crashed | ["ok"] | false | sim crashed: Command '['docker', 'run', '--rm', '-v', 'C:\\dev\\anthropic_hackathon\\runs:/wcEcoli/out', '-e', 'PYTHONPATH=/wcEcoli', '-w', '/wcEcoli', 'wcecoli-si | runs/cellarium/condition_000012/000003 | {} | {} | [] | null | null | null | null | null | null | null | [] | null | null | null | {} | null | null | null | null | null | 8 | true | null |
metabolism_kinetic_objective_weight_0_crash | metabolism_kinetic_objective_weight/minimal|kin_w:0 seed0 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:0 | null | 0 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000000/000000 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_kinetic_objective_weight_1_crash | metabolism_kinetic_objective_weight/minimal|kin_w:0 seed1 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:0 | null | 1 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000000/000001 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_kinetic_objective_weight_2_crash | metabolism_kinetic_objective_weight/minimal|kin_w:0 seed2 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:0 | null | 2 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000000/000002 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_kinetic_objective_weight_3_crash | metabolism_kinetic_objective_weight/minimal|kin_w:0 seed3 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:0 | null | 3 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000000/000003 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_kinetic_objective_weight_1_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1e-4 seed1 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1e-4 | null | 1 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000005/000001 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_kinetic_objective_weight_2_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1e-4 seed2 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1e-4 | null | 2 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000005/000002 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_kinetic_objective_weight_3_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1e-4 seed3 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1e-4 | null | 3 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000005/000003 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_kinetic_objective_weight_0_crash | metabolism_kinetic_objective_weight/minimal|kin_w:0.1 seed0 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:0.1 | null | 0 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000008/000000 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_kinetic_objective_weight_1_crash | metabolism_kinetic_objective_weight/minimal|kin_w:0.1 seed1 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:0.1 | null | 1 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000008/000001 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_kinetic_objective_weight_2_crash | metabolism_kinetic_objective_weight/minimal|kin_w:0.1 seed2 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:0.1 | null | 2 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000008/000002 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_kinetic_objective_weight_3_crash | metabolism_kinetic_objective_weight/minimal|kin_w:0.1 seed3 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:0.1 | null | 3 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000008/000003 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_kinetic_objective_weight_0_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1 seed0 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1 | null | 0 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000009/000000 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_kinetic_objective_weight_1_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1 seed1 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1 | null | 1 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000009/000001 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_kinetic_objective_weight_2_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1 seed2 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1 | null | 2 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000009/000002 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_kinetic_objective_weight_3_crash | metabolism_kinetic_objective_weight/minimal|kin_w:1 seed3 | null | null | null | metabolism_kinetic_objective_weight | minimal|kin_w:1 | null | 3 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_kinetic_objective_weight' is not a validated model variant. | runs/cellarium/metabolism_kinetic_objective_weight_000009/000003 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_0_crash | metabolism_secretion_penalty/minimal|sec_pen:0 seed0 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:0 | null | 0 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000000/000000 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_1_crash | metabolism_secretion_penalty/minimal|sec_pen:0 seed1 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:0 | null | 1 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000000/000001 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_2_crash | metabolism_secretion_penalty/minimal|sec_pen:0 seed2 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:0 | null | 2 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000000/000002 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_3_crash | metabolism_secretion_penalty/minimal|sec_pen:0 seed3 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:0 | null | 3 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000000/000003 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_0_crash | metabolism_secretion_penalty/minimal|sec_pen:1e-3 seed0 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:1e-3 | null | 0 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000004/000000 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_1_crash | metabolism_secretion_penalty/minimal|sec_pen:1e-3 seed1 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:1e-3 | null | 1 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000004/000001 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_2_crash | metabolism_secretion_penalty/minimal|sec_pen:1e-3 seed2 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:1e-3 | null | 2 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000004/000002 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_3_crash | metabolism_secretion_penalty/minimal|sec_pen:1e-3 seed3 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:1e-3 | null | 3 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000004/000003 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_0_crash | metabolism_secretion_penalty/minimal|sec_pen:0.01 seed0 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:0.01 | null | 0 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000007/000000 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_1_crash | metabolism_secretion_penalty/minimal|sec_pen:0.01 seed1 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:0.01 | null | 1 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000007/000001 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_2_crash | metabolism_secretion_penalty/minimal|sec_pen:0.01 seed2 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:0.01 | null | 2 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000007/000002 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_3_crash | metabolism_secretion_penalty/minimal|sec_pen:0.01 seed3 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:0.01 | null | 3 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000007/000003 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_0_crash | metabolism_secretion_penalty/minimal|sec_pen:0.05 seed0 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:0.05 | null | 0 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000009/000000 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_1_crash | metabolism_secretion_penalty/minimal|sec_pen:0.05 seed1 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:0.05 | null | 1 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000009/000001 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_2_crash | metabolism_secretion_penalty/minimal|sec_pen:0.05 seed2 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:0.05 | null | 2 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000009/000002 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
metabolism_secretion_penalty_3_crash | metabolism_secretion_penalty/minimal|sec_pen:0.05 seed3 | null | null | null | metabolism_secretion_penalty | minimal|sec_pen:0.05 | null | 3 | 0 | crashed | null | false | sim crashed (no data): Refusing out-of-envelope design: Perturbation 'metabolism_secretion_penalty' is not a validated model variant. | runs/cellarium/metabolism_secretion_penalty_000009/000003 | null | null | null | null | null | null | null | null | null | null | null | null | null | null | null | 0 | 0 | false | 0 | null | 4 | true | null |
condition_0_1d2ae521 | condition·glc_20mM·s0 | vmnik | vmsi | 1,783,794,963.358033 | condition | glc_20mM | null | 0 | 1 | ok | ["ok"] | true | runs/cellarium/condition_000001/000000 | {"growth_rate": {"mean": 0.0002420471774986793, "min": -0.002336427806929702, "max": 0.00031427210269188987, "first": null, "last": 0.00025325402420660884}, "cell_mass": {"mean": 1737.8979975182783, "min": 1265.035963491068, "max": 2334.396039957032, "first": 1266.3096730856994, "last": 2334.396039957032}, "dry_mass": ... | {"growth_rate": [[0.0, null], [169.0, 0.00023627044363926152], [337.0, 0.00021393728770452395], [506.0, 0.0002721024805668893], [674.0, 0.0002802663906159321], [843.0, 0.0002475847580694358], [1012.0, 0.00022749774790676908], [1180.0, 0.0002478701069350134], [1349.0, 0.0002473292866676274], [1517.0, 0.00025458397883837... | [{"media": "minimal_GLC_20mM", "t0": 0.0, "t1": 2529.0, "n": 2530, "means": {"growth_rate": 0.0002420471774986793, "cell_mass": 1737.8979975182783, "dry_mass": 521.6642097395229, "protein_mass": 245.01950136229323, "rna_mass": 69.57784721352097, "ppgpp_conc": 64.05069640486755, "fba_objective": 0.7456385110620736, "rib... | 0.000242 | 1,737.897998 | 521.66421 | 245.019501 | 69.577847 | 64.050696 | 0.745639 | [{"i": 0, "growth": 0.0002420471774986793, "ppgpp": 64.05069640486755, "divided": true}] | 21.299917 | 0.970919 | 0.099798 | {"translation_ribosome": 0.35057548765469965, "transcription_rnap": 0.0041596647047116115, "stringent_response": 0.0014038902284826188, "glycolysis": 0.03487771373878349, "tca_cycle": 0.014527993403655294, "pentose_phosphate": 0.004857990956700155, "respiration_atp": 0.006874813018496042, "aa_biosynthesis": 0.012632890... | 1 | 1 | true | 0 | 2,529 | null | false | {"2-ISOPROPYLMALATESYN-MONOMER[c]": {"mean": 3037.560869565217, "last": 4006.0, "series": [[0.0, 1956.0], [169.0, 2157.0], [337.0, 2448.0], [506.0, 2672.0], [674.0, 2825.0], [843.0, 2875.0], [1012.0, 2970.0], [1180.0, 3058.0], [1349.0, 3105.0], [1517.0, 3092.0], [1686.0, 3155.0], [1855.0, 3309.0], [2023.0, 3451.0], [21... |
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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, 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.
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.
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