softnanolab/bagel

softnanolab/bagel

Skill Claude CodeCodex

Interactively turn a natural-language protein-design goal into runnable, reviewable BAGEL scripts (the biobagel / import bagel as bg framework). Use this whenever the user describes a protein-design or sequence-optimization problem in plain language and wants BAGEL code — binders, de novo scaffolds, sequence…

softnanolab/bagel

Skill Claude CodeCodex

Look up what a Biohub ESM-C sparse-autoencoder (SAE) feature means — its label, description, top-activating proteins, decoder neighbours, and activation statistics — by querying the Biohub feature-annotation API. Use this whenever the user has SAE feature indices (e.g. from boileroom's SAE model / pooledfeatures) and…