Architecture Docs¶
Comprehensive specification of the Alien Biology system's design and operation. (See ABIO Alienbio User Guide for usage tutorials and API Docs for class and module signatures.)
Alienbio Specification Languages¶
- ABIO Expr Spec — Core language: YAML foundation with tags, scopes, hydration, and evaluation
- M1 Scenario (deleted in M47.7) — Runnable world (molecules, reactions, interface, scoring)
- Experiment — Multi-run experiment over axes
Indexes¶
- ABIO Protocols — Alphabetical index of classes
- ABIO Modules — Alphabetical index of modules
- ABIO Commands — Command reference (CLI and Python)
Subsystems¶
- ABIO infra — Infrastructure: entity base classes, serialization, data management, configuration.
- ABIO biology — Biology: molecules, reactions, pathways, containers, and generators.
- ABIO Suite Runtime — Execution: simulation engine, agent interface, experimentation framework.
Benchmark generation¶
- ABIO Suite Construction — How a suite spec becomes a battery of auto-graded tasks over a small set of verified worlds (realizes the ABIO Inference Bench, sits atop the Scenario Generator PRD).
- ABIO Suite Runtime — The Phase-2 layer that runs an agent against those tasks: the turn loop, the agent Protocols (scripted and live-model), the per-trial record, and the mass-trial sweep.
Project Tracking¶
- ABIO Roadmap — Milestones and release plan
- ABIO Todo — Tasks, open questions, and documentation todos