Can this skill help with gene knockout simulations?

Yes, it provides specific patterns for performing single and double gene/reaction deletions to identify essential genes and analyze metabolic robustness.

How does it handle complex metabolic media changes?

The skill demonstrates how to use Python context managers to temporarily modify growth media or reaction bounds, ensuring that changes are automatically reverted after the simulation is complete.

What is COBRApy used for in metabolic modeling?

COBRApy is a Python library used for constraint-based reconstruction and analysis (COBRA) of metabolic models, allowing researchers to simulate cellular metabolism and predict phenotypic behavior.

Does the COBRApy skill support SBML files?

Absolutely. It includes comprehensive instructions for reading from and writing to SBML, JSON, and YAML formats, which are industry standards for metabolic models.

Is it possible to optimize microbial growth media with this skill?

Yes, the skill includes workflows for calculating minimal media requirements and optimizing component concentrations for specific growth targets.

COBRApy Metabolic Modeling

Name: COBRApy Metabolic Modeling
Author: K-Dense-AI

byK-Dense-AI

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2,188

データサイエンスとML

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

概要

The COBRApy skill empowers researchers and bioinformaticians to conduct genome-scale metabolic modeling directly within Claude. It provides specialized guidance for performing Flux Balance Analysis (FBA), Flux Variability Analysis (FVA), and gene knockout simulations to predict phenotypic behaviors and cellular metabolism. Whether you are optimizing growth media, identifying essential genes, or designing metabolic engineering strategies, this skill offers the implementation patterns and best practices needed to manage complex SBML models and simulate cellular processes efficiently.

主な機能

Growth media optimization and minimal media calculation
Gene and reaction deletion studies for essentiality screening
2,188 GitHub stars
Detailed Flux Variability Analysis (FVA) including loopless options
Comprehensive Flux Balance Analysis (FBA) and Parsimonious FBA
Advanced flux sampling and phenotype phase plane generation

ユースケース

Predicting microbial growth rates and metabolic flux distributions under diverse conditions
Designing and optimizing synthetic media for industrial fermentation processes
Identifying genetic engineering targets by simulating the impact of gene knockouts

概要

主な機能

Growth media optimization and minimal media calculation
Gene and reaction deletion studies for essentiality screening
2,188 GitHub stars
Detailed Flux Variability Analysis (FVA) including loopless options
Comprehensive Flux Balance Analysis (FBA) and Parsimonious FBA
Advanced flux sampling and phenotype phase plane generation

ユースケース

Predicting microbial growth rates and metabolic flux distributions under diverse conditions
Designing and optimizing synthetic media for industrial fermentation processes
Identifying genetic engineering targets by simulating the impact of gene knockouts