# adaptyv

> How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval.

**Use case**: Submit protein sequences to automated cloud lab

**Canonical URL**: https://agentcookbooks.com/skills/adaptyv/

**Topics**: claude-code, skills, science, bioinformatics

**Trigger phrases**: "Adaptyv", "Foundry API", "protein binding assay", "submit protein sequences for characterization"

**Source**: [K-Dense AI](https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/scientific-skills/adaptyv)

**License**: MIT

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## What it does

`adaptyv` is a Claude Code skill from K-Dense AI's [scientific-agent-skills repo](https://github.com/K-Dense-AI/scientific-agent-skills). It turns Claude into a hands-on assistant for Adaptyv Bio's cloud foundry platform — helping you design protein experiments, submit sequences via the REST API or Python SDK, and retrieve assay results programmatically.

The output of a session is working Python code that authenticates against the Foundry API, submits amino acid sequences for experimental characterization (binding, thermostability, expression, fluorescence), and polls for results — all without hardcoding credentials or leaving the terminal.

Adaptyv's automated lab runs assays in approximately 21 days. The skill handles the protocol-side glue so you can focus on which proteins to test rather than how to talk to the platform.

## When to use it

Reach for it when:

- You have a set of designed or engineered protein sequences and want to submit them for BLI, SPR, or thermostability assays at Adaptyv Bio
- You need to build a programmatic pipeline that polls the Foundry API for results and feeds them back into a design loop
- You are setting up environment variables and SDK configuration for a new Adaptyv project and want boilerplate that avoids credential leaks

When *not* to reach for it:

- You need to analyze or visualize already-returned structural data — reach for a structural biology tool instead
- Your sequences are not yet designed and you need a generative model — pair with the `esm` skill first

## Install

Copy the SKILL.md from [scientific-skills/adaptyv](https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/scientific-skills/adaptyv) into `.claude/skills/adaptyv/`.

The skill activates on trigger phrases including "Adaptyv", "Foundry API", "protein binding assay", and "submit protein sequences for characterization".

## What a session looks like

A typical session has three phases:

1. **Environment setup.** Claude reads your project root for a `.env` file and configures `ADAPTYV_API_KEY` and `ADAPTYV_API_URL` using `python-dotenv`. No token touches source control.
2. **Experiment submission.** Claude generates SDK calls using the decorator pattern from `adaptyv-sdk`, targeting the correct assay type and submitting your sequence list with appropriate metadata fields.
3. **Result retrieval.** Claude writes a polling loop or one-shot fetch that returns assay results as structured data (binding scores, Tm values) ready for downstream analysis or re-ranking.

## Receipts

Honest reporting on what `adaptyv` handles well and where it falls short:

**Where it works well:**
- Generating boilerplate API code for first-time Foundry integrations — saves reading through scattered SDK docs
- Multi-sequence batch submission scripts where the same assay parameters apply to a panel of variants
- Setting up CI-style result polling for design-build-test loops

**Where it backfires:**
- The skill cannot simulate assay outcomes — results still take the full lab turnaround cycle
- If the Foundry API schema changes between SDK versions, generated code may reference deprecated fields; always pin the SDK version

**Pattern that works:** run the submission code in a dry-run mode first (log the request payload without posting) to verify sequence formatting and metadata before spending assay budget.

## Source and attribution

Originally authored by [K-Dense, Inc.](https://github.com/K-Dense-AI). The canonical SKILL.md lives in the [`adaptyv` folder](https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/scientific-skills/adaptyv) of the scientific-agent-skills repository.

License: MIT. Install, adapt, and redistribute with attribution preserved.

This page documents the skill from a practitioner's perspective. For the formal spec and updates, defer to the source repo.