Does it support standard bioinformatics file formats?

Yes, it supports SBML (Systems Biology Markup Language), which is the standard for metabolic model exchange, as well as JSON and YAML.

Can I perform gene knockout simulations with this skill?

Yes, the skill includes tools for single and double gene/reaction deletions to help identify essential genes and predict phenotypic changes.

How does it help with metabolic engineering?

It allows you to simulate production envelopes and optimize flux towards specific metabolites, helping to design strains for industrial biotechnology.

What is COBRApy for Claude Code?

It is a specialized skill that allows Claude to use the COBRApy library to analyze and simulate metabolic networks through constraint-based modeling.

COBRApy Metabolic Modeling

Name: COBRApy Metabolic Modeling
Author: Sologa

bySologa

Data Science & ML

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

About

COBRApy is a specialized skill designed for bioinformaticians and systems biologists to perform complex metabolic simulations within Claude Code. It provides a comprehensive suite of tools for genome-scale metabolic modeling, allowing users to execute Flux Balance Analysis (FBA), evaluate gene knockouts, and conduct flux variability studies. By integrating the Python COBRApy library, this skill facilitates the prediction of phenotypic behaviors and the design of metabolic engineering strategies through programmatic model manipulation and advanced optimization techniques.

Key Features

Calculate minimal media requirements and simulate production envelopes
Import and export models in SBML, JSON, and YAML formats for interoperability
Execute Flux Balance Analysis (FBA) and Parsimonious FBA (pFBA) simulations
Perform single and double gene/reaction knockout studies to identify essentiality
Analyze metabolic flux ranges using Flux Variability Analysis (FVA)
0 GitHub stars

Use Cases

Gapfilling metabolic reconstructions to ensure model feasibility and connectivity
Predicting organism growth rates and metabolic fluxes under various environmental conditions
Identifying target genes for metabolic engineering to improve biochemical production

About

Key Features

Calculate minimal media requirements and simulate production envelopes
Import and export models in SBML, JSON, and YAML formats for interoperability
Execute Flux Balance Analysis (FBA) and Parsimonious FBA (pFBA) simulations
Perform single and double gene/reaction knockout studies to identify essentiality
Analyze metabolic flux ranges using Flux Variability Analysis (FVA)
0 GitHub stars

Use Cases

Gapfilling metabolic reconstructions to ensure model feasibility and connectivity
Predicting organism growth rates and metabolic fluxes under various environmental conditions
Identifying target genes for metabolic engineering to improve biochemical production