v2parca vs vEcoli ParCa

Overview

Generated 2026-04-14 15:23:08

v2parca checkpoints: out/sim_data. vEcoli intermediates: /Users/eranagmon/code/vivarium-ecoli/reconstruction/sim_data/intermediates.

Per-step runtime

Step-by-step availability

Step 1 — initialize

Initialize sim_data + scatter

Runtime

Declared data flow

Each Step declares INPUT_PORTS (stores it reads) and OUTPUT_PORTS (stores it writes). Port names are resolved to absolute store paths via STORE_PATH in v2parca/composite.py, and the composite wires each port to the corresponding location in the nested bigraph. The role column shows the description given in the step module (e.g. sim_data.transcription means "mirrors the transcription subsystem on SimulationDataEcoli"; overwrite means the port replaces whatever value lives at that store).

Step purpose: Step 1 — initialize (scatter).

Inputs — reads (0)

(none — this step has no upstream subsystem reads; it only consumes ordering tokens: —)

Outputs — writes (32)

Plus ordering tokens: tick_1 — these enforce Step execution order in the bigraph but carry no data.

Scalar state

Distributions

RNA expression — basal

RNA synthesis prob — basal

RNA deg rates

Cistron deg rates

Protein deg rates

Translation efficiencies

Km endoRNase (transcribed)

Km endoRNase (mature)

Distribution numerical summary

Step 2 — input_adjustments

Pre-fitted adjustments to expression + deg rates

Runtime

Declared data flow

Each Step declares INPUT_PORTS (stores it reads) and OUTPUT_PORTS (stores it writes). Port names are resolved to absolute store paths via STORE_PATH in v2parca/composite.py, and the composite wires each port to the corresponding location in the nested bigraph. The role column shows the description given in the step module (e.g. sim_data.transcription means "mirrors the transcription subsystem on SimulationDataEcoli"; overwrite means the port replaces whatever value lives at that store).

Step purpose: Step 2 — input_adjustments. Apply pre-fitted adjustments to translation efficiencies, RNA expression, and degradation rates.

Inputs — reads (4)

Plus ordering tokens: tick_1 — these enforce Step execution order in the bigraph but carry no data.

Outputs — writes (3)

Plus ordering tokens: tick_2 — these enforce Step execution order in the bigraph but carry no data.

Scalar state

Distributions

RNA expression — basal

RNA synthesis prob — basal

RNA deg rates

Cistron deg rates

Protein deg rates

Translation efficiencies

Km endoRNase (transcribed)

Km endoRNase (mature)

Distribution numerical summary

Step 3 — basal_specs

Build basal cell specifications

Runtime

Declared data flow

Each Step declares INPUT_PORTS (stores it reads) and OUTPUT_PORTS (stores it writes). Port names are resolved to absolute store paths via STORE_PATH in v2parca/composite.py, and the composite wires each port to the corresponding location in the nested bigraph. The role column shows the description given in the step module (e.g. sim_data.transcription means "mirrors the transcription subsystem on SimulationDataEcoli"; overwrite means the port replaces whatever value lives at that store).

Step purpose: Step 3 — basal_specs. Build basal cell specifications.

Inputs — reads (17)

Plus ordering tokens: tick_2 — these enforce Step execution order in the bigraph but carry no data.

Outputs — writes (5)

Plus ordering tokens: tick_3 — these enforce Step execution order in the bigraph but carry no data.

Scalar state

Distributions

RNA expression — basal

RNA synthesis prob — basal

RNA deg rates

Cistron deg rates

Protein deg rates

Translation efficiencies

Km endoRNase (transcribed)

Km endoRNase (mature)

Distribution numerical summary

cell_specs (per-condition max rel Δ)

Step 4 — tf_condition_specs

Per-TF + combined condition cell specs

Runtime

Declared data flow

Each Step declares INPUT_PORTS (stores it reads) and OUTPUT_PORTS (stores it writes). Port names are resolved to absolute store paths via STORE_PATH in v2parca/composite.py, and the composite wires each port to the corresponding location in the nested bigraph. The role column shows the description given in the step module (e.g. sim_data.transcription means "mirrors the transcription subsystem on SimulationDataEcoli"; overwrite means the port replaces whatever value lives at that store).

Step purpose: Step 4 — tf_condition_specs. Build cell specifications for each transcription-factor active/inactive condition and combined conditions.

Inputs — reads (25)

Plus ordering tokens: tick_3 — these enforce Step execution order in the bigraph but carry no data.

Outputs — writes (2)

Plus ordering tokens: tick_4 — these enforce Step execution order in the bigraph but carry no data.

Scalar state

Distributions

RNA expression — basal

RNA synthesis prob — basal

RNA deg rates

Cistron deg rates

Protein deg rates

Translation efficiencies

Km endoRNase (transcribed)

Km endoRNase (mature)

Distribution numerical summary

cell_specs (per-condition max rel Δ)

Only v2parca: ['acetate', 'no_oxygen', 'succinate']. Only vEcoli: ['CPLX0-228__active', 'CPLX0-228__inactive', 'CPLX0-7669__active', 'CPLX0-7669__inactive', 'CPLX0-7796__active', 'CPLX0-7796__inactive', 'EG12123-MONOMER__active', 'EG12123-MONOMER__inactive', 'MONOMER0-155__active', 'MONOMER0-155__inactive', 'MONOMER0-162__active', 'MONOMER0-162__inactive', 'PUTA-CPLX__active', 'PUTA-CPLX__inactive'].

Step 5 — fit_condition

Bulk distributions + translation supply rates

Runtime

Declared data flow

Each Step declares INPUT_PORTS (stores it reads) and OUTPUT_PORTS (stores it writes). Port names are resolved to absolute store paths via STORE_PATH in v2parca/composite.py, and the composite wires each port to the corresponding location in the nested bigraph. The role column shows the description given in the step module (e.g. sim_data.transcription means "mirrors the transcription subsystem on SimulationDataEcoli"; overwrite means the port replaces whatever value lives at that store).

Step purpose: Stage 5: fit_condition — Calculate bulk distributions and translation supply rates for every condition.

Inputs — reads (16)

Plus ordering tokens: tick_4 — these enforce Step execution order in the bigraph but carry no data.

Outputs — writes (2)

Plus ordering tokens: tick_5 — these enforce Step execution order in the bigraph but carry no data.

Scalar state

Distributions

RNA expression — basal

RNA synthesis prob — basal

RNA deg rates

Cistron deg rates

Protein deg rates

Translation efficiencies

Km endoRNase (transcribed)

Km endoRNase (mature)

Distribution numerical summary

cell_specs (per-condition max rel Δ)

Only v2parca: ['acetate', 'no_oxygen', 'succinate']. Only vEcoli: ['CPLX0-228__active', 'CPLX0-228__inactive', 'CPLX0-7669__active', 'CPLX0-7669__inactive', 'CPLX0-7796__active', 'CPLX0-7796__inactive', 'EG12123-MONOMER__active', 'EG12123-MONOMER__inactive', 'MONOMER0-155__active', 'MONOMER0-155__inactive', 'MONOMER0-162__active', 'MONOMER0-162__inactive', 'PUTA-CPLX__active', 'PUTA-CPLX__inactive'].

Step 6 — promoter_binding

TF-promoter binding probabilities (CVXPY)

Runtime

Declared data flow

Each Step declares INPUT_PORTS (stores it reads) and OUTPUT_PORTS (stores it writes). Port names are resolved to absolute store paths via STORE_PATH in v2parca/composite.py, and the composite wires each port to the corresponding location in the nested bigraph. The role column shows the description given in the step module (e.g. sim_data.transcription means "mirrors the transcription subsystem on SimulationDataEcoli"; overwrite means the port replaces whatever value lives at that store).

Step purpose: Step 6 — promoter_binding. Fit transcription-factor binding probabilities and their effect on RNA synthesis.

Inputs — reads (21)

Plus ordering tokens: tick_5 — these enforce Step execution order in the bigraph but carry no data.

Outputs — writes (4)

Plus ordering tokens: tick_6 — these enforce Step execution order in the bigraph but carry no data.

Scalar state

Distributions

RNA expression — basal

RNA synthesis prob — basal

RNA deg rates

Cistron deg rates

Protein deg rates

Translation efficiencies

Km endoRNase (transcribed)

Km endoRNase (mature)

Distribution numerical summary

cell_specs (per-condition max rel Δ)

Only v2parca: ['acetate', 'no_oxygen', 'succinate']. Only vEcoli: ['CPLX0-228__active', 'CPLX0-228__inactive', 'CPLX0-7669__active', 'CPLX0-7669__inactive', 'CPLX0-7796__active', 'CPLX0-7796__inactive', 'EG12123-MONOMER__active', 'EG12123-MONOMER__inactive', 'MONOMER0-155__active', 'MONOMER0-155__inactive', 'MONOMER0-162__active', 'MONOMER0-162__inactive', 'PUTA-CPLX__active', 'PUTA-CPLX__inactive'].

Step 7 — adjust_promoters

Ligand concentrations + RNAP recruitment

Runtime

Declared data flow

Each Step declares INPUT_PORTS (stores it reads) and OUTPUT_PORTS (stores it writes). Port names are resolved to absolute store paths via STORE_PATH in v2parca/composite.py, and the composite wires each port to the corresponding location in the nested bigraph. The role column shows the description given in the step module (e.g. sim_data.transcription means "mirrors the transcription subsystem on SimulationDataEcoli"; overwrite means the port replaces whatever value lives at that store).

Step purpose: Step 7 — adjust_promoters. Tune ligand concentrations and build the RNAP recruitment parameters from the fitted promoter binding probabilities.

Inputs — reads (23)

Plus ordering tokens: tick_6 — these enforce Step execution order in the bigraph but carry no data.

Outputs — writes (3)

Plus ordering tokens: tick_7 — these enforce Step execution order in the bigraph but carry no data.

Scalar state

Distributions

RNA expression — basal

RNA synthesis prob — basal

RNA deg rates

Cistron deg rates

Protein deg rates

Translation efficiencies

Km endoRNase (transcribed)

Km endoRNase (mature)

Distribution numerical summary

cell_specs (per-condition max rel Δ)

Only v2parca: ['acetate', 'no_oxygen', 'succinate']. Only vEcoli: ['CPLX0-228__active', 'CPLX0-228__inactive', 'CPLX0-7669__active', 'CPLX0-7669__inactive', 'CPLX0-7796__active', 'CPLX0-7796__inactive', 'EG12123-MONOMER__active', 'EG12123-MONOMER__inactive', 'MONOMER0-155__active', 'MONOMER0-155__inactive', 'MONOMER0-162__active', 'MONOMER0-162__inactive', 'PUTA-CPLX__active', 'PUTA-CPLX__inactive'].

Step 8 — set_conditions

Per-nutrient dicts + mass rescaling

Runtime

Declared data flow

Each Step declares INPUT_PORTS (stores it reads) and OUTPUT_PORTS (stores it writes). Port names are resolved to absolute store paths via STORE_PATH in v2parca/composite.py, and the composite wires each port to the corresponding location in the nested bigraph. The role column shows the description given in the step module (e.g. sim_data.transcription means "mirrors the transcription subsystem on SimulationDataEcoli"; overwrite means the port replaces whatever value lives at that store).

Step purpose: Step 8 — set_conditions. Rescale mass for soluble metabolites per condition and populate per-nutrient dictionaries on transcription / translation / the top-level expected_dry_mass_increase_dict.

Inputs — reads (11)

Plus ordering tokens: tick_7 — these enforce Step execution order in the bigraph but carry no data.

Outputs — writes (4)

Plus ordering tokens: tick_8 — these enforce Step execution order in the bigraph but carry no data.

Scalar state

Distributions

RNA expression — basal

RNA synthesis prob — basal

RNA deg rates

Cistron deg rates

Protein deg rates

Translation efficiencies

Km endoRNase (transcribed)

Km endoRNase (mature)

Distribution numerical summary

cell_specs (per-condition max rel Δ)

Only v2parca: ['acetate', 'no_oxygen', 'succinate']. Only vEcoli: ['CPLX0-228__active', 'CPLX0-228__inactive', 'CPLX0-7669__active', 'CPLX0-7669__inactive', 'CPLX0-7796__active', 'CPLX0-7796__inactive', 'EG12123-MONOMER__active', 'EG12123-MONOMER__inactive', 'MONOMER0-155__active', 'MONOMER0-155__inactive', 'MONOMER0-162__active', 'MONOMER0-162__inactive', 'PUTA-CPLX__active', 'PUTA-CPLX__inactive'].

Step 9 — final_adjustments

ppGpp kinetics + amino-acid supply constants

Runtime

Declared data flow

Each Step declares INPUT_PORTS (stores it reads) and OUTPUT_PORTS (stores it writes). Port names are resolved to absolute store paths via STORE_PATH in v2parca/composite.py, and the composite wires each port to the corresponding location in the nested bigraph. The role column shows the description given in the step module (e.g. sim_data.transcription means "mirrors the transcription subsystem on SimulationDataEcoli"; overwrite means the port replaces whatever value lives at that store).

Step purpose: Step 9 — final_adjustments. Final expression adjustments, amino-acid supply/export/uptake constants, and ppGpp reaction kinetics parameters.

Inputs — reads (29)

Plus ordering tokens: tick_8 — these enforce Step execution order in the bigraph but carry no data.

Outputs — writes (3)

Plus ordering tokens: tick_9 — these enforce Step execution order in the bigraph but carry no data.