Perform constraint-based metabolic modeling and analysis with COBRApy.
npx skills add https://github.com/Sologa/codex-pipeline --skill cobrapy-sologa
Please help me install this Agent Skill. Skill: cobrapy Source: https://github.com/Sologa/codex-pipeline/tree/main/.codex/skills/cobrapy Command: npx skills add https://github.com/Sologa/codex-pipeline --skill cobrapy-sologa
This Skill empowers users to analyze and simulate metabolic networks, enabling deeper insights into biological systems and facilitating metabolic engineering.
Use the cobrapy skill to load the E. coli core model and predict its maximum growth rate.
High-intent search queries and answers about installing and using this skill.
Flux Balance Analysis (FBA) is performed by loading a metabolic model and calculating optimal flux distributions to predict cellular growth rates. This Skill executes FBA simulations using the COBRApy Python library.
Flux Variability Analysis (FVA) determines the range of possible flux values for each reaction in a metabolic network while maintaining optimal objective values. It is needed to evaluate metabolic model flexibility and identify alternative pathways.
Yes, you can simulate gene knockouts in a metabolic model to identify essential genes for survival. The Skill performs gene and reaction knockout simulations to predict the growth rate of genetically engineered microorganisms.
Yes, this approach supports loading metabolic models in SBML format, along with JSON and YAML formats. You can seamlessly load, save, build, and modify constraint-based metabolic models across these standard file types.
Media optimization for a systems biology model is executed by adjusting environmental constraints and simulating metabolic network responses. This Skill uses COBRApy to facilitate media optimization for metabolic engineering tasks.
TurnaboutHeroPerform ML modeling, causal inference, and time-series analysis with scikit-learn and statsmodels.
dailycafiPredict growth rates and flux distributions for genome-scale models with COBRApy.
hxk622Perform constraint-based metabolic modeling with COBRApy using FBA and FVA.
tassiovalePerform flux balance analysis on genome-scale metabolic models with cobrapy.
