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

0•

数据科学与机器学习

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

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.

主要功能

01Calculate minimal media requirements and simulate production envelopes

02Import and export models in SBML, JSON, and YAML formats for interoperability

03Execute Flux Balance Analysis (FBA) and Parsimonious FBA (pFBA) simulations

04Perform single and double gene/reaction knockout studies to identify essentiality

05Analyze metabolic flux ranges using Flux Variability Analysis (FVA)

060 GitHub stars

使用场景

01Gapfilling metabolic reconstructions to ensure model feasibility and connectivity

02Predicting organism growth rates and metabolic fluxes under various environmental conditions

03Identifying target genes for metabolic engineering to improve biochemical production

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add sologa/codex-pipeline cobrapy

For use in Claude.ai and ChatGPT

Download Skill