[[ABIO]]

Architecture Docs

Comprehensive specification of the Alien Biology system's design and operation. (See Alienbio User Guide for usage tutorials and API Docs for class and module signatures.)

Alienbio Specification Languages

• Spec Language Reference — Core language: YAML foundation with tags, scopes, hydration, and evaluation
• Scenario — 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 execution — Execution: simulation engine, agent interface, experimentation framework.

Project Tracking

• [[ABIO Roadmap]] — Milestones and release plan
• [[ABIO Todo]] — Tasks, open questions, and documentation todos