What can I do with the COBRApy skill in Claude?

This skill allows you to load, manipulate, and simulate genome-scale metabolic models using COBRApy. You can perform growth predictions, gene deletions, flux variability analysis, and media optimization.

Can I use this for gene knockout simulations?

Absolutely. The skill includes core capabilities for single and double gene or reaction deletions, helping you identify essential genes for cellular survival.

Does this skill support standard metabolic model formats?

Yes, it provides implementation patterns for reading and writing models in SBML, JSON, and YAML formats, ensuring compatibility with tools like Escher.

How does it handle complex simulations like flux sampling?

It utilizes optimized sampling methods such as OptGP and ACHR, including best practices for parallel processing to handle computationally intensive tasks efficiently.

COBRApy Metabolic Modeling

Name: COBRApy Metabolic Modeling
Author: jackspace

byjackspace

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数据科学与机器学习

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

关于

The COBRApy skill empowers Claude to manage genome-scale metabolic models and perform sophisticated computational simulations of cellular metabolism within Python environments. It provides standardized patterns for conducting Flux Balance Analysis (FBA), Flux Variability Analysis (FVA), and gene knockout studies, making it an essential tool for bioinformaticians and metabolic engineers. From managing SBML files to sampling the feasible flux space and calculating production envelopes, this skill streamlines complex systems biology workflows with domain-specific best practices.

主要功能

Flux Balance Analysis (FBA) and Parsimonious FBA (pFBA) simulations
Gene and reaction knockout screens for essentiality studies
Flux Variability Analysis (FVA) and flux sampling (OptGP, ACHR)
Comprehensive model management for SBML, JSON, and YAML formats
Automated growth media optimization and minimal media calculation
2 GitHub stars

使用场景

Predicting growth rates and phenotypic behaviors of microorganisms under specific environmental conditions
Visualizing production envelopes and phenotype phase planes for metabolic pathway optimization
Identifying metabolic bottlenecks and essential genes for strain engineering and drug discovery

关于

主要功能

Flux Balance Analysis (FBA) and Parsimonious FBA (pFBA) simulations
Gene and reaction knockout screens for essentiality studies
Flux Variability Analysis (FVA) and flux sampling (OptGP, ACHR)
Comprehensive model management for SBML, JSON, and YAML formats
Automated growth media optimization and minimal media calculation
2 GitHub stars

使用场景

Predicting growth rates and phenotypic behaviors of microorganisms under specific environmental conditions
Visualizing production envelopes and phenotype phase planes for metabolic pathway optimization
Identifying metabolic bottlenecks and essential genes for strain engineering and drug discovery