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Designing network motifs via ODE modeling and NSGA-II.

cell-signaling nsga-ii ode-model optimization synthetic-biology systems-biology

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Name		Name	Last commit message	Last commit date
.github		.github
protosignet		protosignet
tests		tests
.editorconfig		.editorconfig
.gitignore		.gitignore
.pre-commit-config.yaml		.pre-commit-config.yaml
.zenodo.json		.zenodo.json
CONTRIBUTING.md		CONTRIBUTING.md
LICENSE		LICENSE
Makefile		Makefile
README.md		README.md
analyze_prod.py		analyze_prod.py
modal_app.py		modal_app.py
pyproject.toml		pyproject.toml
test_parallel.py		test_parallel.py
test_run.py		test_run.py
tox.ini		tox.ini
uv.lock		uv.lock

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protosignet

Designing network motifs via ODE modeling and NSGA-II.

Getting Started

1. Install UV

$ curl -LsSf https://astral.sh/uv/install.sh | sh

2. Edit objective function and hyperparameters

protosignet/evolve_motifs.py

3. Run NSGA-II to evolve motifs

$ uv run evolve_motifs

4. Plot NSGA-II progress and simulate motif

$ uv run plot_results

About

Designing network motifs via ODE modeling and NSGA-II.

cell-signaling nsga-ii ode-model optimization synthetic-biology systems-biology

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