Welcome to cameo!

Join the chat at https://gitter.im/biosustain/cameo PyPI License Build Status Coverage Status DOI

What is cameo?

Cameo is a high-level python library developed to aid the strain design process in metabolic engineering projects. The library provides a modular framework of simulation and strain design methods that targets developers that want to develop new design algorithms and custom analysis workflows. Furthermore, it exposes a high-level API to users that just want to compute promising strain designs.

Curious? Head over to try.cameo.bio and give it a try.

High-level API (for users)

Compute strain engineering strategies for a desired product in a number of host organisms using the high-level interface (runtime is on the order of hours).

from cameo.api import design


The high-level API can also be called from the command line.

$ cameo design --product vanillin

For more information run

$ cameo --help

Low-level API (for developers)

Find gene knockout targets using evolutionary computation.

from cameo import models
from cameo.strain_design.heuristic import GeneKnockoutOptimization
from cameo.strain_design.heuristic.objective_functions import biomass_product_coupled_yield

model = models.bigg.e_coli_core
obj = biomass_product_coupled_yield(
ko = GeneKnockoutOptimization(model=model, objective_function=obj)
ko.run(max_evaluations=50000, n=1, mutation_rate=0.15, indel_rate=0.185)


Predict heterologous pathways for a desired chemical.

from cameo.strain_design import pathway_prediction
predictor = pathway_prediction.PathwayPredictor(model)
pathways = predictor.run(product="vanillin")


Indices and tables