Adaptyv Bio Foundry API Skill

Adaptyv Bio Foundry API

Adaptyv Bio is a cloud lab that turns protein sequences into experimental data. Users submit amino acid sequences via API or UI; Adaptyv's automated lab runs assays (binding, thermostability, expression, fluorescence) and delivers results in ~21 days.

Quick Start

Base URL: https://foundry-api-public.adaptyvbio.com/api/v1

Authentication: Bearer token in the Authorization header. Tokens are obtained from foundry.adaptyvbio.com sidebar.

When writing code, always read the API key from the environment variable ADAPTYV_API_KEY or from a .env file — never hardcode tokens. Check for a .env file in the project root first; if one exists, use a library like python-dotenv to load it.

export FOUNDRY_API_TOKEN="abs0_..."
curl https://foundry-api-public.adaptyvbio.com/api/v1/targets?limit=3 \
  -H "Authorization: Bearer $FOUNDRY_API_TOKEN"

Every request except GET /openapi.json requires authentication. Store tokens in environment variables or .env files — never commit them to source control.

Python SDK

Install: uv add adaptyv-sdk (falls back to uv pip install adaptyv-sdk if no pyproject.toml exists)

Environment variables (set in shell or .env file):

ADAPTYV_API_KEY=your_api_key
ADAPTYV_API_URL=https://foundry-api-public.adaptyvbio.com/api/v1

Decorator Pattern

from adaptyv import lab

@lab.experiment(target="PD-L1", experiment_type="screening", method="bli")
def design_binders():
    return {"design_a": "MVKVGVNG...", "design_b": "MKVLVAG..."}

result = design_binders()
print(f"Experiment: {result.experiment_url}")

Client Pattern

from adaptyv import FoundryClient

client = FoundryClient(api_key="...", base_url="https://foundry-api-public.adaptyvbio.com/api/v1")

# Browse targets
targets = client.targets.list(search="EGFR", selfservice_only=True)

# Estimate cost
estimate = client.experiments.cost_estimate({
    "experiment_spec": {
        "experiment_type": "screening",
        "method": "bli",
        "target_id": "target-uuid",
        "sequences": {"seq1": "EVQLVESGGGLVQ..."},
        "n_replicates": 3
    }
})

# Create and submit
exp = client.experiments.create({...})
client.experiments.submit(exp.experiment_id)

# Later: retrieve results
results = client.experiments.get_results(exp.experiment_id)

Experiment Types

| Type | Method | Measures | Requires Target | |---|---|---|---| | affinity | bli or spr | KD, kon, koff kinetics | Yes | | screening | bli or spr | Yes/no binding | Yes | | thermostability | — | Melting temperature (Tm) | No | | expression | — | Expression yield | No | | fluorescence | — | Fluorescence intensity | No |

Experiment Lifecycle

Draft → WaitingForConfirmation → QuoteSent → WaitingForMaterials → InQueue → InProduction → DataAnalysis → InReview → Done

| Status | Who Acts | Description | |---|---|---| | Draft | You | Editable, no cost commitment | | WaitingForConfirmation | Adaptyv | Under review, quote being prepared | | QuoteSent | You | Review and confirm the quote | | WaitingForMaterials | Adaptyv | Gene fragments and target ordered | | InQueue | Adaptyv | Materials arrived, queued for lab | | InProduction | Adaptyv | Assay running | | DataAnalysis | Adaptyv | Raw data processing and QC | | InReview | Adaptyv | Final validation | | Done | You | Results available | | Canceled | Either | Experiment canceled |

The results_status field on an experiment tracks: none, partial, or all.

Common Workflows

1. Submit a Binding Screen (Step by Step)

# 1. Find a target
targets = client.targets.list(search="EGFR", selfservice_only=True)
target_id = targets.items[0].id

# 2. Preview cost
estimate = client.experiments.cost_estimate({
    "experiment_spec": {
        "experiment_type": "screening",
        "method": "bli",
        "target_id": target_id,
        "sequences": {"seq1": "EVQLVESGGGLVQ...", "seq2": "MKVLVAG..."},
        "n_replicates": 3
    }
})

# 3. Create experiment (starts as Draft)
exp = client.experiments.create({
    "name": "EGFR binder screen batch 1",
    "experiment_spec": {
        "experiment_type": "screening",
        "method": "bli",
        "target_id": target_id,
        "sequences": {"seq1": "EVQLVESGGGLVQ...", "seq2": "MKVLVAG..."},
        "n_replicates": 3
    }
})

# 4. Submit for review
client.experiments.submit(exp.experiment_id)

# 5. Poll or use webhooks until Done
# 6. Retrieve results
results = client.experiments.get_results(exp.experiment_id)

2. Automated Pipeline (Skip Draft + Auto-Accept Quote)

exp = client.experiments.create({
    "name": "Auto pipeline run",
    "experiment_spec": {...},
    "skip_draft": True,
    "auto_accept_quote": True,
    "webhook_url": "https://my-server.com/webhook"
})
# Webhook fires on each status transition; poll or wait for Done

3. Using Webhooks

Pass webhook_url when creating an experiment. Adaptyv POSTs to that URL on every status transition with the experiment ID, previous status, and new status.

Sequences

Simple format: {"seq1": "EVQLVESGGGLVQPGGSLRLSCAAS"}
Rich format: {"seq1": {"aa_string": "EVQLVESGGGLVQ...", "control": false, "metadata": {"type": "scfv"}}}
Multi-chain: use colon separator — "MVLS:EVQL"
Valid amino acids: A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y (case-insensitive, stored uppercase)
Sequences can only be added to experiments in Draft status

Filtering, Sorting, and Pagination

All list endpoints support pagination (limit 1-100, default 50; offset), search (free-text on name fields), and sorting.

Filtering uses s-expression syntax via the filter query parameter:

Comparison: eq(field,value), neq, gt, gte, lt, lte, contains(field,substring)
Range/set: between(field,lo,hi), in(field,v1,v2,...)
Logic: and(expr1,expr2,...), or(...), not(expr)
Null: is_null(field), is_not_null(field)
JSONB: at(field,key) — e.g., eq(at(metadata,score),42)
Cast: float(), int(), text(), timestamp(), date()

Sorting uses asc(field) or desc(field), comma-separated (max 8):

sort=desc(created_at),asc(name)

Example: filter=and(gte(created_at,2026-01-01),eq(status,done))

Error Handling

All errors return:

{
  "error": "Human-readable description",
  "request_id": "req_019462a4-b1c2-7def-8901-23456789abcd"
}

The request_id is also in the x-request-id response header — include it when contacting support.

Token Management

Tokens use Biscuit-based cryptographic attenuation. You can create restricted tokens scoped by organization, resource type, actions (read/create/update), and expiry via POST /tokens/attenuate. Revoking a token (POST /tokens/revoke) revokes it and all its descendants.

Detailed API Reference

For the full list of all 32 endpoints with request/response schemas, read references/api-endpoints.md.

Agent Skills: Adaptyv Bio Foundry API

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