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:>> ABIO → ABIO Ref → ABIO Protocols

Protocols

Alphabetical listing of all classes in the Alien Biology system, organized by subsystem.

By Subsystem

Subsystem Classes
[[ABIO infra|Infrastructure]] Entity, IO, DAT
[[ABIO Expr Spec|Expr]] Form (Name, Call, Quoted, Include, PyRef), QuotedForm, Env, Ctx, Limits, Registry, Head, TemplateHead, ExprError, GuardViolation, UnsafeSpecError
[[ABIO biology|Biology]] Atom, Chemistry, Compartment, CompartmentTree, ContainerGenerator, Flow, Generator, Molecule, MoleculeGenerator, Pathway, Reaction, ReactionGenerator, WorldSimulator, WorldState
[[ABIO biology|Execution]] Simulator, State, Timeline, World
[[ABIO Suite Construction|Suite construction (M26/M27)]] Motif, CarveResult, Skeleton, SkeletonBlock, TaskArchetype, ObjectiveRecipe, TaskInstance, Question, Answer, AnswerObjective, OutcomeObjective, SuiteSpec, Suite, Draft, Dist, Seed, Vocabulary, Renderable, Op, LLMOp, Predicate, Directive
[[ABIO Suite Runtime|Suite runtime (Phase 2)]] Agent, SessionAgent, ScriptedAgent, LLMAgent, Measure, Intervene, Commit, Wait, ActionOutcome, ReasoningStep, TaskBrief, Affordances, Budget, SimConfig, TrialRecord, ActionRecord, DeliberationTrace, MassTrialRunner, ReliabilityMap, Provenance, ConditionSpec, ExperimentSpec, PowerDesign

The biology and execution rows name the protocols in alienbio.protocols (CompartmentTree, State, World, …); their concrete classes in alienbio.bio carry an Impl suffix (CompartmentTreeImpl, StateImpl, WorldImpl). The Expr row is alienbio.expr (ABIO Expr Python API); the M1 execution stack (Action, Context, Experiment, Measurement, Step, Task, Test, TestHarness, Bio, Interpreter) was deleted in M47.7. The suite rows name concrete dataclasses and Protocols in alienbio.suite — the M26 neutral shadow types (StateVector, Topology, a neutral World/Compartment) were retired in July 2026 (F007) and the suite now builds directly on the biology classes.

A

  • Action (suite) — The closed neutral verb set Measure | Intervene | Commit | Wait; scorers match on type, never on a world's names (suite runtime)
  • ActionOutcome — What the runner tells a SessionAgent after each action: accepted or rejected, and why (suite runtime; M46)
  • ActionRecord — One logged action on a TrialRecord: kind, destructive flag, accepted flag and rejection reason (suite runtime)
  • Affordances — The probe ids a Measure may name and the lever ids an Intervene may name — the declared control surface a brief carries (suite runtime; M46)
  • Agent — The structural Protocol every decision-maker implements: act(observation) -> (Action, reasoning_steps) (suite runtime)
  • Answer — An opaque JSON-ish value tagged by kind (node_set, ordered_path, node_id, scalar, json) (suite; M26)
  • AnswerObjective — Grade a committed Answer against a key with a grader; its sibling OutcomeObjective scores the world trajectory instead (suite; M26)
  • ABIO Atom — Chemical element with symbol, name, and atomic weight

B

  • the M1 Bio facade (deleted in M47.7) — Loading, hydration, and persistence for biology objects in DAT folders
  • Budget — The graded spend cap on the turn loop (unit turns; ladder unlimited/20/12/8/4) — the M32.1 time-pressure dial (suite runtime)

C

  • CarveResult — A motif bound to concrete world nodes plus the extracted ground truth; the pre-F013 name for this was Skeleton (suite; M26)
  • ABIO Chemistry — Container for molecules and reactions forming a chemical system
  • ABIO Compartment — Nestable container for molecules, reactions, and child containers
  • ABIO CompartmentTree — Hierarchical topology of compartments with parent-child relationships
  • ConditionSpec — A dial-vector sampler over orthogonal DialAxis entries with quantization — how a sweep's condition grid is declared (suite runtime; M34.1)

D

  • Draft — What a drafter head returns: (world, task), a 2-tuple with .world / .task (suite; M47.4)
  • DeliberationTrace — The per-trial sequence of DeliberationSteps the runner threads an agent's ReasoningSteps into, read by the M33 trace scorers (suite runtime)
  • Directive — Opaque instruction text a suite Op harness carries; the engine never inspects it (suite; M26)
  • Dist — A seeded distribution (Constant, Uniform, Normal, LogNormal, Choice) — every generator parameter is one (suite; M26)

E

  • Env / Ctx — The Expr environment: scope chain, registry, and the per-node context (seed, path, trust, limits) (expr; M47.1)
  • ExprError — Every Expr failure, a ValueError carrying the node's path (expr; M47.1)
  • ExperimentSpec — One declared experiment, loaded from an !experiment file: axes, drafter, agent, fixed dials, design (suite; M46.5 / M47.4)
  • Entity — Base class for all biology objects

F

  • Form — The five shapes a spec evaluates: literal, Name, data, Call, Quoted (plus the load-time Include / PyRef) (expr; M47.1)
  • ABIO Flow — TransportFlux: amount-conserving transport between any two compartment pools, applied in one rationed pass

H

  • Head / Registry — A registered callable (function, expander, template, special form, guard, constructor, drafter, agent) and the one kind-tagged table of them (expr; M47.1)

I

  • ABIO IO — Entity I/O: prefix bindings, formatting, parsing, persistence

L

  • LLMAgent — A live-model Agent + SessionAgent over the LLMOp seam: briefed at trial start, keeps a turn-history window, opt-in and out of CI (suite runtime; M44/M46)
  • LLMOp — The one model-call seam: schema-validated reply, deterministic cache on (directive, context, seed), retry with a child seed (suite; M26)

M

  • MassTrialRunner — Condition grid × seeded trials → ReliabilityMap, each trial isolated so one failure is a record rather than the end of the sweep (suite runtime; M34)
  • ABIO Molecule — Chemical compound composed of atoms with derived formula and weight
  • Motif — An abstract reaction-network pattern with role slots; a CarveResult binds it to a concrete world (suite; M26)

O

  • ObjectiveRecipe — Opaque protocol turning a carved Skeleton into a task's Question + graded Objective (build_question / build_key / build_distractors / grader_spec) (suite; M27)
  • Op — Opaque callable operation over a context (its scripted form is ScriptedOp) (suite; M26)

P

  • PowerDesign — The statistical design a run commits to (!power): target effect, alpha, power, primary contrast (suite; M46.9)
  • Predicate — Opaque callable over a node, only ever invoked, never inspected — a role constraint / world-validity test (suite; M26)
  • Provenance — What produced a ReliabilityMap: swept axes, base seed, trials per condition, failed-trial count (suite runtime; M34)

Q

  • QuotedForm — A !q form as a value: a Dist (sample(seed)) that also run(bindings)s (expr; M47.1)
  • Question — A structured, opaque JSON-ish question tagged by kind — the agent-facing half of a task, rendered to text by a Renderable (suite; M26)

R

  • ABIO Reaction — Transformation between molecules with reactants, products, effectors
  • ReasoningStep — One opaque reasoning fragment an agent emits while choosing an action (suite runtime)
  • ReliabilityMap — The frozen sweep aggregate: per-cell stats with CIs, 2×2 interactions, effect-size contrasts, every retained TrialRecord, and its Provenance (suite runtime; M34)
  • Renderable — Something that renders itself to text over a vocabulary — deterministic template, never an LLM (suite; M26)

S

  • ScriptedAgent — Deterministic, network-free, seeded step/policy agent — the instrument's zero and what keeps CI green (suite runtime)
  • Seed — A hierarchical deterministic seed; seed.child(label) derives every per-condition, per-trial, per-turn seed (suite; M26)
  • SessionAgent — The optional Protocol an agent implements to be briefed (begin(brief)) and told each action's outcome (notice(outcome)) (suite runtime; M46)
  • SimConfig — Steps and sampling cadence of one simulation burst — one per turn in the runner (suite)
  • ~~[[ABIO simulator|Simulator]]~~ — Execution engine for biology dynamics
  • Skeleton — The F013 recursive SkeletonBlock tree a generator materializes into a world (materialize / validate / oracle); not the pre-F013 Skeleton, now CarveResult (suite; M38)
  • ~~[[ABIO state|State]]~~ — Snapshot of molecule concentrations
  • Suite / SuiteSpec — A materialized suite (worlds + TaskInstances) and the archetype mix it came from (SuiteSpec.per_archetype / seed were unread and are gone, M47.7) (suite; M26/M27)

T

  • TaskArchetype / TaskInstance — The family a task belongs to (with its ObjectiveRecipe and optional drafter), and one concrete task: archetype + world + CarveResult + objective + question (suite; M26/M27)
  • TaskBrief — What the runner tells the agent at trial start: the question, expected answer kind, constitution, affordances, budget and costs, turn and step limits — never the key, target or hidden state (suite runtime; M46)
  • ~~[[ABIO timeline|Timeline]]~~ — Sequence of states with intervention hooks
  • TrialRecord — The frozen unit of observation one agent-run emits: timeline, deliberation trace, action log, objective score, terminal reason, budget accounting, illegal-action count, brief (suite runtime; M40)

V

  • Vocabulary — Injective token↔surface-phrase bijection the NL renderer substitutes through (lossless round-trip) (suite; M26/M27)

W

  • ~~[[ABIO world|World]]~~ — Complete runnable setup with system, generators, initial conditions
  • ABIO WorldSimulator — Multi-compartment simulation engine with reactions and flows
  • ABIO WorldState — Dense concentration storage for multi-compartment simulations