Is flux sampling supported by this skill?

Yes, it includes comprehensive tools for sampling the feasible flux space using OptGP or ACHR methods, including support for parallel processing.

What is COBRApy used for in bioinformatics?

COBRApy is used for constraint-based reconstruction and analysis (COBRA) of metabolic models, helping scientists simulate cellular metabolism and predict phenotypic behaviors.

Can this skill handle SBML metabolic models?

Yes, COBRApy provides robust support for reading and writing models in SBML, JSON, and YAML formats, ensuring compatibility with major systems biology repositories.

How does COBRApy help with metabolic engineering?

It allows users to perform gene knockout simulations, predict growth rates, and analyze flux distributions to identify bottlenecks or optimization targets in metabolic pathways.

What is the difference between FBA and FVA in this context?

FBA (Flux Balance Analysis) finds a single optimal flux distribution for a target objective, while FVA (Flux Variability Analysis) determines the full range of possible flux for each reaction.

COBRApy Bioinformatics

Name: COBRApy Bioinformatics
Author: Activer007

byActiver007

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.

概要

COBRApy is a specialized skill for Claude Code designed to handle complex metabolic modeling tasks using Python-based COBRA methodologies. It enables researchers and developers to manage genome-scale metabolic models, execute Flux Balance Analysis (FBA), perform Flux Variability Analysis (FVA), and conduct comprehensive gene knockout studies. Whether you are predicting cellular growth rates, optimizing metabolic pathways for bio-production, or analyzing metabolic flux distributions, this skill provides the necessary patterns and best practices for robust bioinformatics analysis and SBML model integration.

主な機能

Flux Variability Analysis (FVA) with loopless and optimality constraints
0 GitHub stars
Gene and reaction deletion studies for essentiality screening
Flux Balance Analysis (FBA) and Parsimonious FBA simulations
SBML, JSON, and YAML metabolic model management
Flux sampling and phenotype production envelope calculations

ユースケース

Identifying essential genes and potential targets for metabolic engineering
Designing optimized growth media and minimal media for specific organisms
Simulating microbial growth and metabolic flux under varying environmental conditions

概要

主な機能

Flux Variability Analysis (FVA) with loopless and optimality constraints
0 GitHub stars
Gene and reaction deletion studies for essentiality screening
Flux Balance Analysis (FBA) and Parsimonious FBA simulations
SBML, JSON, and YAML metabolic model management
Flux sampling and phenotype production envelope calculations

ユースケース

Identifying essential genes and potential targets for metabolic engineering
Designing optimized growth media and minimal media for specific organisms
Simulating microbial growth and metabolic flux under varying environmental conditions