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stat-research-orchestrator
// Orchestrate a statistical research pipeline centered on formal problem formulation, method proposal, theoretical analysis, experimental evaluation, comparison, and final result synthesis.
// Orchestrate a statistical research pipeline centered on formal problem formulation, method proposal, theoretical analysis, experimental evaluation, comparison, and final result synthesis.
Run Flux Balance Analysis (FBA) and related constraint-based simulations using COBRApy. Covers standard FBA, parsimonious FBA (pFBA), Flux Variability Analysis (FVA), loopless FBA, gene/reaction knockouts, and carbon source swapping. Outputs flux distributions and CSV files.
Analyse FBA flux distributions to extract biological insights. Covers gene essentiality, phenotypic phase planes, flux sampling, pathway-level aggregation, secretion product prediction, and production of publication- quality figures.
Build or load a genome-scale metabolic model (GSMM) using COBRApy. Covers loading from BIGG, constructing minimal models from scratch, setting medium constraints, and exporting validated .json model files.
Validate a COBRApy genome-scale metabolic model for mass/charge balance, stoichiometric consistency, biomass producibility, dead-end metabolites, thermodynamic loops, and GPR rule formatting. Outputs a structured validation report with errors and warnings.
Plan publishable constraint-based metabolic modelling studies when the user has a broad biological or metabolic-engineering topic but no concrete dataset, organism, model, or hypothesis. Selects feasible BiGG/COBRA models, objectives, perturbations, analyses, metrics, figures, and risk controls before FBA code is generated.
Orchestrate the full metabolic flux analysis pipeline from model loading to phenotype prediction and publication figures. Triggers when the user provides an organism name, BIGG model ID, or custom reaction list and wants end-to-end metabolic modelling run automatically.
| name | stat-research-orchestrator |
| description | Orchestrate a statistical research pipeline centered on formal problem formulation, method proposal, theoretical analysis, experimental evaluation, comparison, and final result synthesis. |
| metadata | {"category":"domain","trigger-keywords":"statistics,statistical research,problem formulation,method proposal,theory,experiments,comparison,results","applicable-stages":"1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20","priority":"1"} |
Coordinates the full statistical research pipeline. This is not a code-first benchmark workflow. The pipeline begins with formal problem formulation and requires theory before final comparisons and conclusions.
Topic prompt / topic file / dataset description
-> [stat-problem-formulator] formal problem, notation, assumptions, targets
-> [stat-method-proposer] proposed method, baselines, diagnostics, ablations
-> [stat-theory-analyzer] theoretical properties, proof sketches, predictions
-> [stat-experiment-designer] experiments, code, metrics, manifest
-> [stat-comparison-analyst] method comparison, theory-vs-experiment check
-> [stat-result-synthesizer] final report, conclusions, limitations
-> [stat-quality-auditor] formulation/theory/evidence audit
Provide the topic source and any requirements. Wait for:
progress/<TOPIC_ID>/step0_problem_formulation.md
Read:
Do not proceed if the target or assumptions are undefined.
Provide the problem formulation. Wait for:
progress/<TOPIC_ID>/step1_method_proposal.md
Read:
Provide the formulation and method proposal. Wait for:
progress/<TOPIC_ID>/step2_theory_analysis.md
Read:
Theory can be partial, but the report must honestly label what is proven, heuristic, or only experimentally supported.
Provide formulation, method, and theory. Wait for:
progress/<TOPIC_ID>/step3_experimental_evaluation.md
Read:
Provide theory predictions and experiment outputs. Wait for:
progress/<TOPIC_ID>/step4_comparison.md
Read:
Provide all previous artifacts. Wait for:
progress/<TOPIC_ID>/step5_result_synthesis.md
Read:
Audit the whole research chain:
Wait for:
progress/<TOPIC_ID>/step6_quality_audit.md
progress/<TOPIC_ID>/step0_problem_formulation.md# Step 0: Problem Formulation
## Status: PASS / FAIL
## Topic ID: <TOPIC_ID>
## Research Question
...
## Formal Data Model
...
## Target / Estimand
...
## Assumptions
- ...
## Claims / Hypotheses
- ...
## Evaluation Criteria
- ...
## Theory Targets
- ...
## Blocking Ambiguities
- ...
progress/<TOPIC_ID>/step1_method_proposal.md# Step 1: Method Proposal
## Status: PASS / FAIL
## Proposed Method
...
## Baselines
- ...
## Diagnostics
- ...
## Ablations
- ...
## Method-to-Claim Map
- ...
progress/<TOPIC_ID>/step2_theory_analysis.md# Step 2: Theoretical Analysis
## Status: PASS / PARTIAL / FAIL
## Definitions
...
## Main Claims
- ...
## Proof Sketches
- ...
## Assumptions Required
- ...
## Predicted Empirical Patterns
- ...
## Limitations
- ...
progress/<TOPIC_ID>/step3_experimental_evaluation.md# Step 3: Experimental Evaluation
## Status: PASS / FAIL
## Config
experiments/<TOPIC_ID>/config.yaml
## Code
- ...
## Experiments
- ...
## Metrics
experiments/<TOPIC_ID>/results/metrics.json
## Manifest
experiments/<TOPIC_ID>/results/run_manifest.json
## Warnings
- ...
progress/<TOPIC_ID>/step4_comparison.md# Step 4: Comparison
## Status: PASS / FAIL
## Baseline Comparisons
- ...
## Ablation Findings
- ...
## Theory vs Experiment
- ...
## Claim Verdicts
experiments/<TOPIC_ID>/results/claim_verdicts.json
progress/<TOPIC_ID>/step5_result_synthesis.md# Step 5: Result Synthesis
## Status: PASS / FAIL
## Paper
experiments/<TOPIC_ID>/report/paper.md
## README
experiments/<TOPIC_ID>/README.md
## Final Claims
- ...
## Limitations
- ...
progress/<TOPIC_ID>/step6_quality_audit.md# Step 6: Quality Audit
## Status: PASS / WARN / FAIL
## Formulation Check
- ...
## Theory Check
- ...
## Experiment Check
- ...
## Comparison Check
- ...
## Blocking Issues
- ...