E. coli acetate overflow metabolism phase map under glucose and oxygen limitation
Domain: biology (systems-biology, constraint-based-modelling, phase-plane-analysis)
Topic: E. coli acetate overflow metabolism phase map under glucose and oxygen limitation
Venue: ARC-Bench Biology 2026
Headline metric: primary_metric (maximize)

Research briefing:
Overflow acetate secretion in E. coli is a canonical constraint-based
modelling phenotype. A credible CPU-scale study loads a validated E. coli
genome-scale model, fixes a glucose-minimal medium, sweeps glucose and oxygen
uptake bounds, computes growth and major secretion products, and identifies
the transition from respiratory growth to overflow/fermentative by-product
secretion.

The research question is: under which glucose and oxygen uptake regimes does
E. coli switch from primarily respiratory growth to acetate-secreting overflow
metabolism, and how robust is that regime boundary across FBA and pFBA?

Hypotheses:
statement: The selected E. coli BIGG model grows on aerobic glucose-minimal medium with a positive biomass objective and no infeasible solver status., statement: A two-dimensional glucose-vs-oxygen phase plane contains distinct regimes with high oxygen/low acetate and low oxygen/high acetate secretion., statement: pFBA reduces total internal flux while preserving the same growth-rate regime boundaries to within a small tolerance.

Experiment design:
research_question: Under which glucose and oxygen uptake regimes does E. coli switch from respiratory growth to acetate overflow?
conditions: name: aerobic_glucose_reference
description: Wild-type E. coli iJO1366 or iAF1260 on glucose-minimal medium with oxygen available., name: glucose_oxygen_phase_plane
description: Grid over glucose uptake and oxygen uptake bounds; compute biomass, acetate, ethanol, lactate, succinate, and CO2 exchange fluxes., name: pfba_phase_plane_check
description: Run pFBA on the same grid or a representative subset and compare growth plus secretion regimes.
baselines: High-oxygen glucose condition is the respiratory baseline., Zero-oxygen glucose condition is the fermentative baseline.
metrics: name: growth_rate_1_per_h
direction: maximize
description: Biomass objective flux for each nutrient grid point., name: acetate_flux_mmol_gDW_h
direction: characterize
description: Acetate exchange secretion flux., name: overflow_boundary_o2_bound
direction: estimate
description: Approximate oxygen bound below which acetate secretion exceeds a chosen threshold., name: pfba_total_flux_norm
direction: minimize
description: Total absolute flux under pFBA.
datasets: name: E. coli GSMM
source: BIGG iJO1366 or iAF1260 via cobra.io.load_model
compute_requirements: gpu_required: no
estimated_wall_clock_sec: 1800

Requirements:
type: artifact
description: A results.json file exists with primary_metric, metrics, hypotheses, summary, and structured_results., type: artifact
description: A machine-readable phase-plane table exists with glucose_bound, oxygen_bound, growth_rate, and acetate_flux columns., type: artifact
description: A PNG or PDF heatmap/phase-plane figure exists with glucose and oxygen axes and units., type: numeric
description: results.json metrics MUST contain a numeric value for `aerobic_glucose_growth_rate_1_per_h` (or an equivalent aerobic_growth_*_1_per_h key) that is non-null, finite, and positive. The aerobic reference growth rate must be reported, otherwise H1 cannot be evaluated., type: discussion
description: Each of hypotheses.h1, hypotheses.h2, hypotheses.h3 in results.json MUST have an explicit `supported` boolean and a `details` string of at least 40 characters describing the evidence used to reach that verdict.
, type: discussion
description: The overflow boundary and its mechanistic basis are discussed — why E. coli switches to acetate-secreting overflow at the identified nutrient threshold. Acceptable inside summary, phase_plane_interpretation, or a separate writeup field., type: discussion
description: The solver backend (cobra optlang interface name + version) and COBRApy version are reported in results.json. Required for reproducibility but not for scientific correctness.

Scoring rubric:
requirements: A credible constraint-based E. coli acetate-overflow phase-plane study that loads a validated BIGG model, sets glucose and oxygen medium bounds, sweeps a two-dimensional nutrient grid, reports growth and by-product secretion, and interprets the acetate overflow boundary.
judging_note: Score biological substance and quantitative reproducibility over exact thresholds. iJO1366, iAF1260, or a comparable curated E. coli GSMM are acceptable.
sub_tasks: requirements: The COBRApy implementation defines the model, medium, phase-plane grid, FBA/pFBA runs, and secretion extraction.
sub_tasks: requirements: Loads a validated E. coli BIGG model, explicitly sets glucose and oxygen exchange bounds, and names the biomass objective.
task_category: Code Development
finegrained_task_category: Method Implementation, requirements: Constructs a two-dimensional glucose-by-oxygen grid with at least 8 values per axis and restores model state between conditions.
task_category: Code Development
finegrained_task_category: Experimental Setup, requirements: Extracts biomass plus acetate, ethanol, lactate, succinate, CO2, and O2/glucose exchange fluxes where present.
task_category: Code Development
finegrained_task_category: Method Implementation, requirements: Runs pFBA on the full grid or a justified representative subset and records total absolute flux.
task_category: Code Development
finegrained_task_category: Method Implementation, requirements: Execution produces stable phase-plane artifacts without infeasible or missing-condition failures dominating the study.
sub_tasks: requirements: At least 90% of grid points solve to optimal or biologically expected zero-growth status with explicit handling.
task_category: Code Execution
finegrained_task_category: Evaluation, Metrics & Benchmarking, requirements: Mass-balance check passes for the loaded model; no non-physical secretion fluxes appear under aerobic conditions without explicit justification (e.g. acetate secretion is zero under high-oxygen/low-glucose conditions in the reference FBA); biomass flux is positive under aerobic glucose reference. This is the biology-validity gate equivalent to physics-validity checks in the physics rubric.
task_category: Code Execution
finegrained_task_category: Evaluation, Metrics & Benchmarking, requirements: Writes results.json and a CSV/TSV phase-plane table with nutrient bounds, growth, and secretion fluxes.
task_category: Code Execution
finegrained_task_category: Logging, Analysis & Presentation, requirements: The analysis identifies and explains acetate-overflow regimes with figures and quantitative criteria.
sub_tasks: requirements: Reports reference aerobic glucose growth and confirms model feasibility and positive biomass production. Score 100% if a positive finite biomass flux is reported for aerobic glucose with optimal solver status; 67% if growth is positive but solver status is not verified; 33% if only feasibility is stated without a numeric growth value; 0% otherwise.
task_category: Result Analysis
finegrained_task_category: Logging, Analysis & Presentation, requirements: Quantifies an acetate secretion boundary or threshold across oxygen/glucose regimes and distinguishes respiratory vs overflow conditions. Score 100% if an acetate-overflow boundary is quantified (O2 or glucose uptake threshold stated) with ≥2 distinct secretion regimes visible in the phase-plane table; 67% if overflow is identified without a quantified boundary; 33% if only one secretion regime is described; 0% otherwise.
task_category: Result Analysis
finegrained_task_category: Logging, Analysis & Presentation, requirements: Compares FBA and pFBA growth/secretion regimes and explains where they agree or differ. Score 100% if FBA and pFBA growth rates are numerically compared and total flux norms are reported for both; 67% if only growth rates are compared without flux-norm comparison; 33% if pFBA was run but not compared to FBA; 0% otherwise.
task_category: Result Analysis
finegrained_task_category: Logging, Analysis & Presentation, requirements: Produces at least one labelled heatmap or contour plot for growth and acetate secretion with units.
task_category: Result Analysis
finegrained_task_category: Logging, Analysis & Presentation, requirements: The README or results writeup discusses each hypothesis outcome, characterises the acetate-overflow regime boundary with quantitative support, and gives a one-paragraph mechanistic interpretation of why E. coli shifts from respiratory to acetate-secreting overflow metabolism at the identified nutrient threshold.
task_category: Result Analysis
finegrained_task_category: Logging, Analysis & Presentation, requirements: The model ID, medium, grid values, solver, and thresholds are recorded for rerun reproducibility.
sub_tasks: requirements: The loaded E. coli GSMM is either persisted (models/<model_id>.json) or pinned by BIGG model ID and source URL in the writeup; a downstream user can locate the exact model object used.
task_category: Code Development
finegrained_task_category: Reproducibility, requirements: Saves model ID, objective reaction, nutrient grid, and secretion threshold in config or results metadata.
task_category: Code Development
finegrained_task_category: Reproducibility, requirements: Records solver backend, tolerance, COBRApy version, and rerun consistency for the aerobic reference point.
task_category: Code Development
finegrained_task_category: Reproducibility