Which model formats are supported?

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

What types of optimization can it perform?

It supports standard Flux Balance Analysis (FBA), parsimonious FBA (pFBA) for minimizing total flux, and geometric FBA for finding central solutions.

Can I simulate gene knockouts with this skill?

Yes, the skill provides tools for single and double gene or reaction deletions to predict how these changes affect cellular growth and metabolism.

COBRApy Metabolic Modeling

Name: COBRApy Metabolic Modeling
Author: Zehong-Wang

byZehong-Wang

0•

数据科学与机器学习

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

This skill empowers Claude to perform advanced systems biology research using the COBRApy library. It enables the simulation of cellular metabolism through Flux Balance Analysis (FBA) and Flux Variability Analysis (FVA), allowing researchers to predict phenotypic behaviors and growth rates. Users can conduct virtual gene knockout studies, optimize growth media, and perform flux sampling to understand metabolic distributions. With full support for SBML, JSON, and YAML model formats, this skill streamlines the computational workflow for designing microbial strains and analyzing genome-scale metabolic networks.

主要功能

01Flux Variability Analysis (FVA) and OptGP flux sampling

02Metabolic model management for SBML, JSON, and YAML formats

03Flux Balance Analysis (FBA) and Parsimonious FBA (pFBA) simulations

040 GitHub stars

05Comprehensive gene and reaction knockout analysis

06Automated growth media and minimal media optimization

使用场景

01Designing optimized microbial strains for industrial metabolic engineering and production

02Identifying essential genes and potential drug targets through virtual deletion studies

03Predicting bacterial growth rates and metabolic fluxes under varying environmental conditions

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos cobrapy

For use in Claude.ai and ChatGPT

Download Skill