Does it support flux sampling?

Yes, it includes methods like OptGP and ACHR for sampling the feasible flux space to understand flux distributions and uncertainty.

What is COBRApy used for in Claude Code?

COBRApy allows Claude to perform constraint-based metabolic modeling, including analyzing metabolic fluxes, simulating gene knockouts, and predicting cellular behavior.

Is it suitable for metabolic engineering?

Absolutely, it features production envelope calculations and gapfilling to help design and optimize metabolic pathways for industrial or research purposes.

Can I import my own metabolic models?

Yes, the skill supports loading models in SBML, JSON, and YAML formats, as well as providing access to several standard test models like E. coli.

How does this skill handle gene knockouts?

It provides functions for single and double gene/reaction deletions, using context managers to test growth impacts without permanently altering the base model.

COBRApy Metabolic Modeling

Name: COBRApy Metabolic Modeling
Author: jimmc414

byjimmc414

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324

Data Science & ML

Performs constraint-based reconstruction and analysis of metabolic models for systems biology and metabolic engineering.

About

COBRApy is a specialized skill for Claude Code designed to facilitate systems biology research through constraint-based metabolic modeling. It enables researchers and bioinformaticians to perform complex simulations like Flux Balance Analysis (FBA) and Flux Variability Analysis (FVA), conduct gene knockout studies, and optimize growth media. By leveraging the COBRApy library, this skill streamlines the process of loading, building, and analyzing genome-scale metabolic models (GEMs) directly within the Claude environment, making it an essential tool for predicting phenotypic behaviors and designing metabolic engineering strategies.

Key Features

Automated Flux Balance Analysis (FBA) and Parsimonious FBA
324 GitHub stars
Comprehensive Gene and Reaction Deletion/Knockout Studies
Model Management with SBML, JSON, and YAML support
Flux Variability Analysis (FVA) and Flux Sampling
Growth Media Optimization and Minimal Media Calculation

Use Cases

Identifying essential genes for drug targeting or metabolic engineering
Designing optimal growth media and predicting phenotypic behavior in microorganisms
Predicting cell growth rates and metabolic fluxes under various environmental conditions

About

Key Features

Automated Flux Balance Analysis (FBA) and Parsimonious FBA
324 GitHub stars
Comprehensive Gene and Reaction Deletion/Knockout Studies
Model Management with SBML, JSON, and YAML support
Flux Variability Analysis (FVA) and Flux Sampling
Growth Media Optimization and Minimal Media Calculation

Use Cases

Identifying essential genes for drug targeting or metabolic engineering
Designing optimal growth media and predicting phenotypic behavior in microorganisms
Predicting cell growth rates and metabolic fluxes under various environmental conditions