Bijux Proteomics

bijux-proteomics is split on purpose. It is easier to understand, review, and trust when runtime authority, program contracts, intelligence, evidence, and lab planning stay separate instead of dissolving into one vague codebase.

This landing page is for orientation. A reader should be able to skim it, decide where their question belongs, and move on without needing a meeting.

How To Read The Site

flowchart LR
    start["Start with the question you have"]
    repo["Repository handbook<br/>shared rules and system fit"]
    runtime["agentic-proteins<br/>runtime orchestration and replay authority"]
    foundation["bijux-proteomics-foundation<br/>shared schema and serialization primitives"]
    core["bijux-proteomics-core<br/>program definitions and lifecycle contracts"]
    intelligence["bijux-proteomics-intelligence<br/>candidate ranking and explainability"]
    knowledge["bijux-proteomics-knowledge<br/>evidence, claims, and contradiction handling"]
    lab["bijux-proteomics-lab<br/>experiment planning and outcome loops"]

    start --> repo
    start --> runtime
    start --> foundation
    start --> core
    start --> intelligence
    start --> knowledge
    start --> lab

Start Here

• Open the Repository Handbook when the question crosses package boundaries or touches shared repository rules.
• Open one product package when the question is about owned behavior, public surfaces, workflows, or proof inside that package.

Package Handbooks

• agentic-proteins owns runtime execution, orchestration, replay, and operator-facing runtime surfaces.
• bijux-proteomics-foundation owns schema compatibility helpers and canonical payload serialization primitives.
• bijux-proteomics-core owns program definitions, constraints, and lifecycle contract models.
• bijux-proteomics-intelligence owns candidate scoring, ranking, and explainable decision outputs.
• bijux-proteomics-knowledge owns evidence records, claim state, and contradiction resolution boundaries.
• bijux-proteomics-lab owns experiment planning, assay outcomes, and closed-loop lab-facing artifacts.

The root docs should shorten conversations, not create new documentation ceremony.