File size: 11,230 Bytes
7a72c74 | 1 2 | {"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}}, "annotations": {"collateral": {"any": 1069, "full": 913, "max_full": 11, "max_full_cell": "T2/wzyE_KO/acetate", "max_full_genes": ["rffC", "rffG", "rffH", "rffM", "wecA", "wecB", "wecC", "wecE", "wecF", "wzxE", "wzzE"], "single_cells": 2752, "working_single_cells": 1982}, "conditions": {"glucose_labels": 19364, "relabelled": 19715, "relabelled_regulation": {"acetate -> basal": 32, "basal -> acetate": 32, "basal -> no_oxygen": 32, "basal -> plus_cytidine": 32, "basal -> plus_indole": 32, "basal -> with_aa": 126, "no_oxygen -> plus_arabinose": 32, "no_oxygen -> with_aa": 32, "plus_arabinose -> with_aa": 32, "plus_indole -> basal": 32, "plus_nitrate -> no_oxygen": 32, "succinate -> basal": 32, "with_aa -> basal": 128, "with_aa -> plus_nitrate": 32, "with_aa -> succinate": 32}, "sinusoidal": 384}, "confound": {"double_knockout": {"8ff93a58 c462ae99": 103, "8ff93a58 c47683e1": 58, "8ff93a58 ddc88250": 14, "b1750cf0 c41efd75": 11776}, "single_knockout": {"8ff93a58 c47683e1": 83937}, "wildtype_media": {"8ff93a58 ddc88250": 29, "b1750cf0 18a908d2": 4, "b1750cf0 c41efd75": 604, "b1750cf0 e319d09f": 4}}, "designs": {"canonical_trajectories": 81393, "cells": 3896, "cross_family_designs": 2, "designs": 2701, "families": {"double_knockout": {"cells": 150, "designs": 75, "label_group_cells": 0, "label_groups": 0, "redundant_cells": 75}, "dynamic_media": {"cells": 204, "designs": 78, "label_group_cells": 204, "label_groups": 78, "redundant_cells": 126}, "regulation": {"cells": 0, "designs": 0, "label_group_cells": 0, "label_groups": 0, "redundant_cells": 0}, "single_knockout": {"cells": 1650, "designs": 661, "label_group_cells": 918, "label_groups": 369, "redundant_cells": 989}, "wildtype_media": {"cells": 4, "designs": 1, "label_group_cells": 0, "label_groups": 0, "redundant_cells": 3}}, "mixed_provenance_designs": 20, "multi_cell_designs": 817, "single_knockout_designs": 1763}, "knockout": {"cells": 3727, "partial": {"cells": 1145, "families": {"double_knockout": {"cells": 195, "trajectories": 6211}, "dynamic_media": {"cells": 180, "trajectories": 4889}, "single_knockout": {"cells": 770, "trajectories": 24452}}, "trajectories": 35552}, "trajectories": 111829}, "partition": {"redundant_glucose_copy": {"cells": 360, "trajectories": 10723}, "redundant_operon_copy": {"cells": 431, "trajectories": 12562}, "relabel_mid_run": {"cells": 174, "trajectories": 5346}, "relabel_t0": {"cells": 1141, "conditions": {"acetate": 11083, "succinate": 10924, "with_aa": 12882}, "trajectories": 34889}, "rerun": {"cells": 1145, "trajectories": 35552}, "usable": {"any_collateral_cells": 158, "any_collateral_trajectories": 4665, "cells": 364, "collateral_cells": 125, "collateral_trajectories": 3667, "conditions": {"basal": 10759}, "families": {"double_knockout": 1144, "dynamic_media": 32, "single_knockout": 9583}, "shift_at_t0": 0, "trajectories": 10759, "viable": 9879}, "withdraw": {"cells": 112, "trajectories": 1998}}, "shifts": {"shift_at_t0": 61660, "shift_at_t0_by_condition": {"minimal -> acetate": 19468, "minimal -> fumarate": 32, "minimal -> malate": 32, "minimal -> minus_calcium": 32, "minimal -> minus_magnesium": 32, "minimal -> no_oxygen": 32, "minimal -> plus_gallate": 32, "minimal -> plus_indole": 32, "minimal -> plus_nitrate": 32, "minimal -> plus_nitrite": 32, "minimal -> plus_quercetin": 32, "minimal -> plus_tungstate": 32, "minimal -> succinate": 19222, "minimal -> with_aa": 22618}, "unfitted_mid_run": {"cells": 366, "trajectories": 11457}, "unfitted_t0": {"cells": 1992, "trajectories": 61660}}, "withdrawn": {"born_into": {"minimal_minus_phosphate": 418, "minimal_no_glucose": 1547}, "born_into_divided": {"minimal_minus_phosphate": 0, "minimal_no_glucose": 898}, "cells": 200, "trajectories": 3565}}, "builder_commit": "db3415a72f007937b7ba463e05472b8e2a6255f4", "builder_dirty": false, "built_at": "2026-10-30T22:50:30+00:00", "cell_health": {"one_second_divisions": 153, "rule": "viable = divided and not translation_collapse and not short_trajectory (n_steps <= 10)", "short_trajectory": 160, "termination_class": {"equilibrium_unstable": 6, "fba_infeasible": 3, "negative_counts": 2647, "none": 112545, "time_limit": 1973}, "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}, "viable": {"not_viable": 8969, "viable": 108205, "viable_null": 0}}, "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": 82689886494, "families": {"double_knockout": {"bytes": 8834921380, "files": 5, "rows": 3154907, "trajectories": 11951}, "dynamic_media": {"bytes": 11714776392, "files": 7, "rows": 4739949, "trajectories": 18599}, "regulation": {"bytes": 1689737741, "files": 1, "rows": 552844, "trajectories": 2046}, "single_knockout": {"bytes": 59938007205, "files": 35, "rows": 23209171, "trajectories": 83937}, "wildtype_media": {"bytes": 512443776, "files": 1, "rows": 173523, "trajectories": 641}}, "files": 49, "rows": 31830394, "stride": 10, "trajectories": 117174}, "expression_1s": {"bytes": 327374894759, "families": {"double_knockout": {"bytes": 35015027772, "files": 20, "rows": 31390535, "trajectories": 11951}, "dynamic_media": {"bytes": 46399835623, "files": 30, "rows": 47151419, "trajectories": 18599}, "regulation": {"bytes": 6543237433, "files": 4, "rows": 5501785, "trajectories": 2046}, "single_knockout": {"bytes": 237395746938, "files": 145, "rows": 230981330, "trajectories": 83937}, "wildtype_media": {"bytes": 2021046993, "files": 2, "rows": 1726776, "trajectories": 641}}, "files": 201, "rows": 316751845, "stride": 1, "trajectories": 117174}, "metabolism": {"bytes": 90290988719, "families": {"double_knockout": {"bytes": 9122907254, "files": 5, "rows": 3154907, "trajectories": 11951}, "dynamic_media": {"bytes": 13506859556, "files": 7, "rows": 4739949, "trajectories": 18599}, "regulation": {"bytes": 1601554846, "files": 1, "rows": 552844, "trajectories": 2046}, "single_knockout": {"bytes": 65557375917, "files": 34, "rows": 23209171, "trajectories": 83937}, "wildtype_media": {"bytes": 502291146, "files": 1, "rows": 173523, "trajectories": 641}}, "files": 48, "rows": 31830394, "stride": 10, "trajectories": 117174}, "metabolism_1s": {"bytes": 880313345607, "families": {"double_knockout": {"bytes": 88921110892, "files": 45, "rows": 31390535, "trajectories": 11951}, "dynamic_media": {"bytes": 131592724635, "files": 67, "rows": 47151419, "trajectories": 18599}, "regulation": {"bytes": 15581700311, "files": 8, "rows": 5501785, "trajectories": 2046}, "single_knockout": {"bytes": 639324807480, "files": 325, "rows": 230981330, "trajectories": 83937}, "wildtype_media": {"bytes": 4893002289, "files": 3, "rows": 1726776, "trajectories": 641}}, "files": 448, "rows": 316751845, "stride": 1, "trajectories": 117174}, "summary": {"bytes": 35024613, "families": {"double_knockout": {"bytes": 3965433, "files": 1, "pathway_columns": 13, "rows": 11951, "trajectories": 11951}, "dynamic_media": {"bytes": 6218467, "files": 1, "pathway_columns": 13, "rows": 18599, "trajectories": 18599}, "regulation": {"bytes": 736033, "files": 1, "pathway_columns": 13, "rows": 2046, "trajectories": 2046}, "single_knockout": {"bytes": 23862117, "files": 1, "pathway_columns": 13, "rows": 83937, "trajectories": 83937}, "wildtype_media": {"bytes": 242563, "files": 1, "pathway_columns": 13, "rows": 641, "trajectories": 641}}, "files": 5, "rows": 117174, "stride": 1, "trajectories": 117174}}, "deg_rates": {"5558948af4ad806f21d7c80c": {"kb_sha256": "8ff93a58576f484edfd6fea641eeeb4fc554b52b97da49f4d8b275ca74496667", "mrna_units": {"ceiling": 7, "determined": 2293, "floor": 246, "imputed": 587, "total": 3133}, "not_a_fit_pct_basal_mrna_expression": 12.216}, "fa6a9ebd4b1c988a36ef9fa1": {"kb_sha256": "b1750cf04409c37ebce9d4d3009daeae0779dd66508812c2807744d83baf1ab7", "mrna_units": {"ceiling": 7, "determined": 2293, "floor": 246, "imputed": 587, "total": 3133}, "not_a_fit_pct_basal_mrna_expression": 12.216}}, "export_checks": {"attempts": 585870, "failed": 0, "meaning": "trajectory x config writes checked against the export gates (rows landed, steps contiguous, counts valid); says nothing about whether the cell was healthy: see cell_health"}, "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}}, "held_back": [], "kb_sha256": {"5558948af4ad806f21d7c80c": "8ff93a58576f484edfd6fea641eeeb4fc554b52b97da49f4d8b275ca74496667", "fa6a9ebd4b1c988a36ef9fa1": "b1750cf04409c37ebce9d4d3009daeae0779dd66508812c2807744d83baf1ab7"}, "simulator_commits": {"18a908d28303c2feeba161e962c049e4f712454e": 4, "5f5fa5f4fe2302af12385528d176f4d73c4bf3a6": 88, "c41efd7561d40316e5e83b20e3fb27316845b0bc": 14376, "c462ae99c47d24c327a0311edd785f664d8038bc": 4371, "c47683e19614b17e9c022762a238a1b36aa12dd2": 84229, "ddc88250ad5c3ab07872c46888cd18f0fd3d32e6": 14102, "e319d09f3749168155d246b103b7d37ba492ec63": 4}, "splits": {"split_by_lineage": {"test": 11739, "train": 93703, "val": 11732}, "split_by_tu": {"test": 14298, "train": 90837, "val": 12039}}, "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}, "trna_channels": {"channels": ["aa_pool_size", "ntp_pool_size", "trna_charged_fraction"], "families": {"double_knockout": 0, "dynamic_media": 0, "regulation": 0, "single_knockout": 0, "wildtype_media": 0}, "not_recorded": 117174, "recorded": 0}, "version": "1.0.0-rc2-pre"}
|