Data & ReproScientific VisualizationFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-workflows-metabolic-modeling-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

Metabolic model reconstruction → FBA → simulation → visualization.

OpenClawNanoClawAnalysisWritingbio-workflows-metabolic-modeling-pipeline🧠 bioos extended suitebioos extended bioinformatics suitemetabolic

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-workflows-metabolic-modeling-pipeline

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Complete workflow for genome-scale metabolic modeling: from protein sequences to flux predictions and phenotype analysis.
carve genome.faa -o model_draft.xml.

Source Doc

Excerpt From SKILL.md

Prerequisites

Required data:

Protein FASTA file from genome annotation
BiGG universal model (downloaded by CarveMe)

With gram type specification (improves biomass composition)

carve genome.faa -o model_draft.xml --gram-neg

Gap-fill for specific media

carve genome.faa -o model_draft.xml --gram-neg --gapfill M9 python import cobra

model = cobra.io.read_sbml_model('model_draft.xml') print(f'Model: {model.id}') print(f'Reactions: {len(model.reactions)}') print(f'Metabolites: {len(model.metabolites)}') print(f'Genes: {len(model.genes)}')

Use cases

Use bio-workflows-metabolic-modeling-pipeline to prepare publication-quality figures.
Apply bio-workflows-metabolic-modeling-pipeline when results need clear visual communication.