bio-workflows-metabolic-modeling-pipeline - Orchestrate genome-scale metabolic modeling
Orchestrates reconstruction, quality control, curation, media-constrained flux analysis, gene essentiality, and context-specific modeling from protein FASTA and expression data.
Tags
Updated: 2026-10-07Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Reconstruct genome-scale models
- Run MEMOTE quality checks
- Curate and gap-fill models
- Constrain media before FBA
- Predict flux distributions
- Analyze gene essentiality
- Build context-specific models
Inputs
- Protein FASTA file
- Target growth medium
- Genome annotation
- Expression data
- Universal reaction model
- Reconstruction tool choice
Outputs
- Reconstructed metabolic model
- MEMOTE quality report
- Curated metabolic model
- Gap-filled reaction set
- FBA and FVA flux predictions
- Essential gene list
- Context-specific model
- Condition-specific fluxes
Requirements
- Python environment
- COBRApy 0.29 or newer
- CarveMe and memote
- NumPy, pandas, matplotlib, seaborn
- DIAMOND
- MILP solver for CarveMe