# A-Alpha Bio

> A-Alpha Bio is a Seattle biotechnology company that measures, predicts and engineers protein-protein interactions.
> Its experimental platform AlphaSeq reprograms yeast mating to quantify millions of binding affinities in a single
> experiment; its computational platform AlphaBind predicts and optimizes antibody-antigen binding from sequence.
> Atlas, launched July 2026, is the company's data platform: ML-ready protein interaction "Data Blocks" available for
> licensing, on-demand custom data generation, and a quarterly-release consortium. Atlas is backed by a public HTTP
> API — the Atlas Data Product API.

Generated: 2026-08-06
Method: generated (A-Alpha Bio publishes no llms.txt — /llms.txt returns 404 on www.aalphabio.com and
api.atlas.aalphabio.com, and soft-404s into the SPA shell on atlas.aalphabio.com)
Source: https://github.com/api-evangelist/a-alpha-bio

## What an agent can call without credentials

The Atlas Data Product API at `https://api.atlas.aalphabio.com` serves three operations anonymously:

- `GET /api/v1/datasets?include_locked=true&include_coming_soon=true` — the public Data Block catalogue.
  IMPORTANT: with default flags this returns an empty `objects` array. You must set `include_locked=true`.
- `GET /api/v1/datasets/{id}` — metadata for one Data Block.
- `GET /api/v1/datasets/{id}/datacard` — the structured Data Card (executive summary, ML guidance, biology/assay).

Everything else — CSV data, CSV schema, structure (.cif) files, figures — returns
`401 {"detail":"Missing token"}` without an Atlas bearer token.

## API

- OpenAPI 3.1.0 (live): https://api.atlas.aalphabio.com/openapi.json
- OpenAPI (harvested verbatim): openapi/a-alpha-bio-atlas-data-product-openapi-original.json
- OpenAPI (refined, servers + tags declared): openapi/a-alpha-bio-atlas-datasets-openapi.yml
- Overlay of API Evangelist enhancements: overlays/a-alpha-bio-atlas-datasets-overlay.yaml
- Base URL: https://api.atlas.aalphabio.com
- Version: path segment `/api/v1`; specification `info.version` 0.0.43

### Operations

- `listDatasets` — GET /api/v1/datasets — list accessible datasets (flags: all_versions, include_locked, include_coming_soon)
- `getDataset` — GET /api/v1/datasets/{id} — dataset metadata (query: version)
- `getDatasetDatacard` — GET /api/v1/datasets/{id}/datacard — structured Data Card (query: version)
- `getDatasetData` — GET /api/v1/datasets/{id}/data — CSV via pre-signed S3 URL (query: max_rows, mode, redirect, version)
- `getDatasetSchema` — GET /api/v1/datasets/{id}/schema — pandas-ready column schema (query: mode, version)
- `listDatasetStructures` — GET /api/v1/datasets/{id}/structures — structure filenames (query: version)
- `downloadDatasetStructures` — GET /api/v1/datasets/{id}/structures/download — pre-signed URL for a zip of all structures
- `getDatasetStructure` — GET /api/v1/datasets/{id}/structures/{filename} — one structure file
- `getDatasetFigure` — GET /api/v1/datasets/{id}/figures/{tab}/{filename} — a Data Card figure image

## Authentication

- HTTP bearer JWT: `Authorization: Bearer <token>`
- Issued by an AWS Cognito user pool via the hosted-UI authorization-code flow the Atlas web app runs
  (scopes: openid, email, profile, aws.cognito.signin.user.admin)
- CLI clients use the browser-assisted login-code flow at https://atlas.aalphabio.com/cli-login
- Detail: authentication/a-alpha-bio-authentication.yml

## Conventions an agent should know

- No pagination — `GET /api/v1/datasets` returns the whole collection in `objects[]`. No cursor, no Link header.
- No rate-limit headers and no documented 429. Back off conservatively.
- No request-id header on any response — there is nothing to quote in a support ticket.
- Errors are NOT RFC 9457. The envelope is `{"detail": <string>}`, except 422 where `detail` is an ARRAY of
  Pydantic validation objects. Check the type of `detail` before treating it as a string.
- Binary payloads are handed off as pre-signed S3 URLs, by default as a 302. Pass `redirect=false` on
  `getDatasetData` to get `{"url": "..."}` as JSON instead.
- Pin `version` explicitly. Omitting it resolves to latest, which makes a training run non-reproducible across a
  dataset re-release.
- Undocumented but live: `GET /health` returns `{"status":"ok"}`.
- Detail: conventions/a-alpha-bio-conventions.yml

## Data model

Single-root. Everything hangs off Dataset (a "Data Block"), which owns data modes, a Data Card, a CSV schema,
structure files and figures. `product_kind` is the commercial model as an API field —
`open-source` | `consortium` | `licensable` | `exclusive`.

- data-model/a-alpha-bio-data-model.yml
- json-schema/a-alpha-bio-dataset-item.json
- json-schema/a-alpha-bio-datacard.json
- json-schema/a-alpha-bio-dataset-schema.json

## Agent skills

- skills/_index.yml
- skills/a-alpha-bio-browse-atlas-catalog.md
- skills/a-alpha-bio-load-data-block-into-pandas.md

## What does not exist

Recorded so an agent does not go looking. All probed 2026-08-06.

- No MCP server. `/mcp`, `/api/v1/mcp`, `/api/mcp`, `/sse` all 404 on the API host; `mcp.aalphabio.com` does not resolve.
  A derived candidate tool map is at mcp/a-alpha-bio-mcp.yml — it is a proposal, not an A-Alpha Bio product.
- No A2A agent card. `/.well-known/agent-card.json` and `/.well-known/agent.json` 404 on every host.
- No `/.well-known/` documents at all — no security.txt, no openid-configuration, no oauth metadata.
- No GraphQL endpoint.
- No AsyncAPI, webhooks, or event surface of any kind.
- No status page, no SLA, no changelog, no deprecation policy.
- No published SDK or client library on npm, PyPI, or the A-Alpha-Bio GitHub org.
- No developer documentation site. The only machine-readable contract is the served OpenAPI.

## Company

- Website: https://www.aalphabio.com/
- Atlas platform: https://atlas.aalphabio.com/
- Technology (AlphaSeq + AlphaBind): https://www.aalphabio.com/technology/
- Applications: https://www.aalphabio.com/applications/
- About: https://www.aalphabio.com/about/
- News: https://www.aalphabio.com/media/
- Blog: https://aalphabio.substack.com/
- GitHub: https://github.com/A-Alpha-Bio (one public repo — alphabind, the AlphaBind model and pre-print code)
- Contact: https://www.aalphabio.com/contact/
- Terms: https://www.aalphabio.com/terms-of-service/
- Privacy: https://www.aalphabio.com/privacy-notice/

## About this file

This is a third-party profile maintained by API Evangelist, not an A-Alpha Bio publication.
https://apievangelist.com/about/where-our-data-comes-from