GRASP Library Designer

Codon-optimize GRASP (Farley et al., NAR 2025) binder DNA for Golden Gate assembly.

PyPI: grasp-library-designer · Import: grasp_library

Open in Google Colab

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Notebook	Open
One-shot (one RNA → free GGA oligos)
Library (42-module redesign → GAP compile)

Direct links:

• One-shot: https://colab.research.google.com/github/JustABiologist/grasp-library-designer/blob/main/grasp_oneshot_designer.ipynb
• Library: https://colab.research.google.com/github/JustABiologist/grasp-library-designer/blob/main/grasp_library_designer.ipynb

Each notebook installs with:

%pip install -q -U "grasp-library-designer>=0.1.3"

Bundled GenBank modules and Potapov ligation tables ship inside the PyPI package (materialize_project()).

Install locally

pip install grasp-library-designer
# optional notebook extras
pip install "grasp-library-designer[notebook]"

from grasp_library import materialize_project, build_default_config, LigationFidelityCalculator

project = materialize_project()  # ./grasp_library_project + GenBank
config = build_default_config(project / "input")
print(LigationFidelityCalculator(25, 18).set_fidelity(["AATG", "GATA"]))

From a blank Colab / Jupyter, you can also drop the Forms notebooks onto disk:

%pip install -q -U grasp-library-designer
from grasp_library import write_notebook
write_notebook("oneshot")   # or "library"
# then open the written .ipynb from the file browser

What each notebook does

Hard constraints (library path): protein fixed (synonymous codons only); coding Golden Gate overhang bases stay locked in coding_mask. Objectives: ligation fidelity (Potapov / GGAssembler), codon optimality, synthesis fitness.

Develop from source

git clone https://github.com/JustABiologist/grasp-library-designer.git
cd grasp-library-designer
python3 -m venv .venv
source .venv/bin/activate
pip install -e ".[notebook,dev]"

Package layout

grasp_library/                 # installable Python package
  data/profiles/.../genbank/   # bundled GRASP GenBank modules
  notebooks/                   # Colab Forms notebooks (also at repo root)
  paths.py                     # materialize_project()
  ...
third_party/dawdlib_golden_gate/   # Potapov ligation fidelity (AGPL)

License

AGPL-3.0 (required by the vendored GGAssembler / dawdlib ligation engine). See LICENSE and THIRD_PARTY_LICENSES.md.

GRASP sequences: Farley et al., Nucleic Acids Res. 2025.