What model formats are supported by the COBRApy skill?

The skill supports standard systems biology formats including SBML (.xml), JSON for Escher compatibility, and YAML for human-readability.

Does it support flux sampling for uncertainty analysis?

Absolutely. It includes capabilities for sampling the feasible flux space using methods like OptGP and ACHR to understand flux distributions.

Can I use this skill to identify essential genes?

Yes, it provides automated workflows for single and double gene deletion studies to determine which genes are critical for cellular growth.

How does the skill handle temporary model changes?

It utilizes Python context managers, allowing you to make temporary modifications to bounds or objectives that automatically revert after the analysis.

COBRApy Metabolic Modeling

Name: COBRApy Metabolic Modeling
Author: Microck

byMicrock

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Data Science & ML

Performs constraint-based metabolic modeling and simulation for systems biology and metabolic engineering applications.

About

COBRApy is a specialized Python library designed for the reconstruction and analysis of genome-scale metabolic models. This skill empowers Claude to manage complex model structures, execute Flux Balance Analysis (FBA), perform Flux Variability Analysis (FVA), and conduct systematic gene deletion studies. It is a critical tool for bioinformaticians and researchers seeking to predict phenotypic behaviors, optimize metabolic pathways, and simulate cellular metabolism within a computational environment.

Key Features

Execute Flux Balance Analysis (FBA) and Parsimonious FBA simulations
Conduct comprehensive Flux Variability Analysis (FVA) and flux sampling
Perform large-scale gene and reaction knockout screens for essentiality testing
Import and export models in SBML, JSON, and YAML formats
Calculate minimal media requirements and generate production envelopes
81 GitHub stars

Use Cases

Identifying metabolic targets for bioengineering and industrial production
Analyzing the impact of genetic perturbations on cellular metabolism
Predicting organism growth rates and metabolic fluxes under diverse conditions

About

Key Features

Execute Flux Balance Analysis (FBA) and Parsimonious FBA simulations
Conduct comprehensive Flux Variability Analysis (FVA) and flux sampling
Perform large-scale gene and reaction knockout screens for essentiality testing
Import and export models in SBML, JSON, and YAML formats
Calculate minimal media requirements and generate production envelopes
81 GitHub stars

Use Cases

Identifying metabolic targets for bioengineering and industrial production
Analyzing the impact of genetic perturbations on cellular metabolism
Predicting organism growth rates and metabolic fluxes under diverse conditions