| name | mfa-pipeline-orchestrator |
| description | 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. |
| metadata | {"category":"domain","trigger-keywords":"metabolic flux analysis,MFA,FBA,COBRApy,BIGG,metabolic engineering,genome-scale metabolic model,knockout,yield,phenotype prediction","applicable-stages":"8,9,10,11,12,13,14,15,16,17","priority":"1"} |
MFA Pipeline Orchestrator
Overview
Coordinates all mfa-agent sub-agents in sequence, tracking progress via progress/ markdown files so any failed step can be resumed independently.
Full pipeline:
Model source (BIGG ID / custom reactions)
→ [model-builder] models/<Model>.json + validation report
→ [fba-runner] simulations/fba_fluxes.csv + scan_summary.json
→ [flux-analyzer] analysis/essentiality.csv + phase_plane.png
→ [metabolic-pheno-analyzer] output/figures/*.pdf + yield table
Workflow
Step 0: Parse User Request
Extract and record in progress/step0_inputs.md:
- Model source (BIGG ID or custom)
- Organism and condition (aerobic/anaerobic, carbon source, concentration)
- Objective reaction (biomass or product)
- Gene knockouts to apply
- Analysis goals (essentiality, phase plane, yield optimisation, WT vs. mutant comparison)
- Target product (if yield analysis requested)
Step 1: Invoke model-builder
Provide: model source, medium constraints, objective, knockouts.
Wait for .
Read: model file path, WT growth rate, model statistics.
