S. cerevisiae ethanol yield under oxygen limitation and carbon-source changes
Domain: biology (systems-biology, metabolic-engineering, constraint-based-modelling)
Topic: S. cerevisiae ethanol yield under oxygen limitation and carbon-source changes
Venue: ARC-Bench Biology 2026
Headline metric: primary_metric (maximize)

Research briefing:
Yeast ethanol fermentation is a natural extension beyond E. coli while still
staying inside BIGG/COBRApy constraint-based modelling. A credible study
loads iMM904 or a comparable yeast GSMM, validates growth on glucose, sweeps
oxygen availability, compares glucose and alternative carbon sources, and
quantifies ethanol secretion and yield.

Hypotheses:
statement: The yeast model grows on glucose-minimal medium and produces a feasible FBA solution., statement: Ethanol secretion/yield increases as oxygen uptake is restricted relative to fully aerobic growth., statement: Carbon-source swaps produce distinct growth and ethanol-yield profiles, with glucose supporting stronger fermentation than at least one alternative carbon source.

Experiment design:
research_question: How do oxygen limitation and carbon source alter predicted ethanol secretion and yield in S. cerevisiae?
conditions: name: yeast_glucose_reference
description: S. cerevisiae iMM904 or comparable model on glucose-minimal medium., name: oxygen_sweep
description: Sweep oxygen uptake from anaerobic/low oxygen to aerobic while glucose uptake is fixed., name: carbon_source_swap
description: Compare glucose, fructose, galactose, glycerol, and acetate when supported by the model.
baselines: Aerobic glucose condition., Anaerobic or oxygen-limited glucose condition.
metrics: name: growth_rate_1_per_h
direction: maximize
description: Biomass flux., name: ethanol_flux_mmol_gDW_h
direction: maximize
description: Ethanol exchange secretion flux., name: ethanol_yield_per_carbon_uptake
direction: maximize
description: Ethanol secretion divided by substrate uptake.
datasets: name: S. cerevisiae iMM904
source: BIGG iMM904 via cobra.io.load_model if available, or documented local SBML/JSON yeast model.
compute_requirements: gpu_required: no
estimated_wall_clock_sec: 1800

Requirements:
type: artifact
description: results.json contains yeast model ID, metrics, hypotheses, and structured oxygen/carbon-source results., type: artifact
description: A machine-readable oxygen-sweep table exists with oxygen bound, growth, ethanol flux, and yield., type: artifact
description: A carbon-source comparison table exists, including unsupported sources marked explicitly., type: artifact
description: At least one oxygen-vs-ethanol or carbon-source yield figure exists with units., 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 ethanol-yield response to oxygen and carbon source is discussed mechanistically — why oxygen restriction increases ethanol yield and how carbon-source metabolism shapes fermentation. Acceptable inside summary, structured_results, 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 S. cerevisiae ethanol-yield study that loads a yeast GSMM, validates growth, sweeps oxygen uptake, swaps carbon sources, and reports ethanol secretion/yield with interpretable figures.
judging_note: The main challenge is adapting the pipeline beyond E. coli while remaining within COBRApy/BIGG capabilities. Accept iMM904 or another documented yeast GSMM.
sub_tasks: requirements: The code implements yeast model loading, medium setup, oxygen sweep, carbon-source swap, and ethanol-yield calculations.
sub_tasks: requirements: Loads iMM904 or comparable yeast model, identifies biomass, glucose, oxygen, and ethanol exchange reactions, and validates positive reference growth.
task_category: Code Development
finegrained_task_category: Method Implementation, requirements: Sweeps oxygen uptake across at least 8 values while keeping substrate uptake defined and restoring state between runs.
task_category: Code Development
finegrained_task_category: Experimental Setup, requirements: Compares at least 4 carbon sources where model reactions exist and explicitly records unsupported sources.
task_category: Code Development
finegrained_task_category: Experimental Setup, requirements: Calculates ethanol yield using absolute substrate uptake and separates yield from raw secretion flux.
task_category: Code Development
finegrained_task_category: Method Implementation, requirements: Execution produces oxygen-sweep and carbon-source artifacts without crashing.
sub_tasks: requirements: Reference glucose condition is optimal and at least 80% of supported oxygen/carbon conditions solve or are clearly marked infeasible.
task_category: Code Execution
finegrained_task_category: Evaluation, Metrics & Benchmarking, requirements: Mass-balance check passes for the yeast GSMM; no non-physical fluxes appear under aerobic glucose reference (e.g. ethanol secretion should be low under full aerobic conditions); biomass flux is positive under yeast glucose-minimal 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, oxygen_sweep.csv, and carbon_source_comparison.csv or equivalent structured outputs.
task_category: Code Execution
finegrained_task_category: Logging, Analysis & Presentation, requirements: Results quantify oxygen and substrate effects on ethanol secretion/yield.
sub_tasks: requirements: Reports yeast reference growth with model ID and medium definition. Score 100% if positive yeast biomass flux and ethanol secretion are both reported under aerobic glucose-minimal medium with optimal solver status and a named model ID; 67% if growth is positive but ethanol is not reported; 33% if feasibility is stated without numeric values; 0% otherwise.
task_category: Result Analysis
finegrained_task_category: Logging, Analysis & Presentation, requirements: Quantifies how ethanol flux or yield changes as oxygen decreases and identifies the low-oxygen fermentation regime. Score 100% if ethanol flux or yield is non-decreasing as oxygen uptake decreases across ≥6 of 8 oxygen-sweep points; 67% if non-decreasing over ≥4 of 8 points; 33% if the trend is described without a quantitative grid; 0% otherwise.
task_category: Result Analysis
finegrained_task_category: Logging, Analysis & Presentation, requirements: Compares growth and ethanol yield across carbon sources with a biological interpretation. Score 100% if at least 3 carbon sources are compared with distinct numeric ethanol yields and a biological interpretation; 67% if 2 sources are compared with numeric differences; 33% if the comparison is qualitative or only one carbon source produces positive growth; 0% otherwise.
task_category: Result Analysis
finegrained_task_category: Logging, Analysis & Presentation, requirements: Produces labelled figures for oxygen sweep and/or carbon-source yield comparison.
task_category: Result Analysis
finegrained_task_category: Logging, Analysis & Presentation, requirements: The README or results writeup discusses each hypothesis outcome, names the oxygen regime and carbon source that maximise ethanol yield, and gives a one-paragraph mechanistic interpretation of why oxygen restriction switches yeast from respiratory growth to fermentative ethanol production.
task_category: Result Analysis
finegrained_task_category: Logging, Analysis & Presentation, requirements: Model source, medium, oxygen grid, carbon-source reactions, solver, and versions are documented.
sub_tasks: requirements: The loaded yeast GSMM is either persisted (models/<model_id>.json) or pinned by BIGG model ID, version, 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 reaction IDs, bounds, grid values, and carbon-source list in config or results metadata.
task_category: Code Development
finegrained_task_category: Reproducibility, requirements: Records COBRApy, solver, model source/version, and rerun consistency for reference growth.
task_category: Code Development
finegrained_task_category: Reproducibility