Analyze and simulate metabolic models with flux balance analysis using COBRApy.
npx skills add https://github.com/galeep/plugin-place --skill cobrapy-galeep
Please help me install this Agent Skill. Skill: cobrapy Source: https://github.com/galeep/plugin-place/tree/main/plugins/sci-materials-chemistry/skills/cobrapy Command: npx skills add https://github.com/galeep/plugin-place --skill cobrapy-galeep
This Skill addresses the challenges in systems biology and metabolic engineering by enabling the construction and analysis of metabolic models using COBRApy.
To get started with COBRApy, install it using the command: uv pip install cobra==0.31.1. Then, load a model with model = load_model("path/to/model") and perform an FBA with solution = model.optimize().
High-intent search queries and answers about installing and using this skill.
Perform flux balance analysis (FBA) by loading a metabolic model and executing the optimize method to calculate optimal metabolic fluxes. This Skill automates the FBA simulation process using COBRApy for systems biology workflows.
Flux variability analysis (FVA) determines the range of possible flux values for each reaction in a metabolic model while maintaining optimal growth. Use FVA when analyzing genetic changes and identifying alternative metabolic pathways in constraint-based models.
Yes, metabolic models can be loaded, saved, and managed in SBML, JSON, and YAML formats. This Skill handles model management across these standard file formats for constraint-based metabolic modeling workflows.
GLPK is required by default, but you can use alternative linear programming solvers like CPLEX or Gurobi. This Skill supports these solver dependencies to perform constraint-based metabolic model optimization and analysis.
Model gapfilling identifies and adds missing metabolic reactions to incomplete models using COBRApy. This Skill performs gapfilling to complete metabolic networks, allowing successful flux balance analysis and simulation of biological systems.
The best way to analyze genetic changes on metabolic fluxes is running FBA and FVA on metabolic models. This Skill uses constraint-based approaches to simulate genetic perturbations and evaluate their impact on biological pathways.
AlterLab-IEUAutomate COBRApy metabolic modeling workflows for FBA, FVA, and strain design.
RamanEbrahimiBuild and analyze metabolic pathway models with cobrapy in Python.
tondevrelFormulate and solve linear, mixed-integer, and non-linear optimization models with Pyomo.
silversteinPerform constraint-based metabolic modeling with FBA, FVA, and flux sampling.
