What types of models does the COBRApy skill support?

It supports genome-scale metabolic models in SBML (Systems Biology Markup Language), JSON, and YAML formats, and includes built-in access to standard models like E. coli.

Is it possible to optimize growth media components?

Absolutely, the skill can calculate minimal media requirements and simulate metabolic behavior under different nutrient uptake constraints.

Can I perform gene knockouts with this skill?

Yes, the skill provides tools for single and double gene or reaction deletions, helping you identify essential genes and predict phenotypic changes after mutations.

Does this skill support flux sampling for uncertainty analysis?

Yes, it includes capabilities for sampling the feasible flux space using methods like OptGP and ACHR to understand flux distributions beyond simple optimization.

COBRApy Metabolic Modeling

Name: COBRApy Metabolic Modeling
Author: pur3v4d3r

bypur3v4d3r

•

データサイエンスとML

Performs constraint-based metabolic modeling and systems biology simulations using the COBRApy framework.

概要

COBRApy is a specialized skill designed for systems biologists and metabolic engineers to perform genome-scale metabolic modeling and analysis. It enables advanced flux simulations such as Flux Balance Analysis (FBA) and Flux Variability Analysis (FVA), facilitates in silico gene knockout studies, and manages complex metabolic models in SBML, JSON, or YAML formats. This skill is essential for researchers looking to predict cellular phenotypes, optimize microbial production strains, and analyze metabolic network behavior under various environmental and genetic constraints directly within their development environment.

主な機能

Metabolic flux sampling and production envelope calculation
Automated growth media and minimal media optimization
1 GitHub stars
Flux Balance Analysis (FBA) and Flux Variability Analysis (FVA)
In silico gene and reaction knockout simulations
Genome-scale metabolic model management and SBML support

ユースケース

Predicting growth rates and metabolic fluxes in microbial organisms
Optimizing metabolic pathways for industrial bio-production and metabolic engineering
Identifying essential genes through systematic computational knockout screens

概要

主な機能

Metabolic flux sampling and production envelope calculation
Automated growth media and minimal media optimization
1 GitHub stars
Flux Balance Analysis (FBA) and Flux Variability Analysis (FVA)
In silico gene and reaction knockout simulations
Genome-scale metabolic model management and SBML support

ユースケース

Predicting growth rates and metabolic fluxes in microbial organisms
Optimizing metabolic pathways for industrial bio-production and metabolic engineering
Identifying essential genes through systematic computational knockout screens