Skip to content

Architecture Docs → ABIO execution

Timeline

Sequence of states with intervention hooks.

Overview

Timeline records the history of states throughout a simulation run, supporting intervention hooks for applying perturbations at specific times.

Property Type Description
states List[State] Recorded state history
interventions List[tuple] (time, function) pairs to apply
events List[tuple] (time, description) event log
Method Returns Description
add_intervention(time, fn) None Schedule intervention at time
get_state_at(time) State Get state at or before time

Discussion

Usage Example

from alienbio import Timeline

timeline = Timeline()

# Schedule an intervention
def add_glucose(state):
    state.set("glucose", state.get("glucose") + 100)
    return state

timeline.add_intervention(time=50.0, fn=add_glucose)

# Access history
final_state = timeline.states[-1]
state_at_25 = timeline.get_state_at(25.0)

Interventions

Interventions are functions that transform state at specific times:

# Drug addition at t=100
timeline.add_intervention(100.0, lambda s: add_drug(s, "insulin", 50.0))

# Stress response at t=200
timeline.add_intervention(200.0, lambda s: apply_stress(s, factor=2.0))

Protocol

from typing import Protocol, List, Tuple, Callable

class Timeline(Protocol):
    """Sequence of states with interventions."""

    states: List[State]
    interventions: List[Tuple[float, Callable[[State], State]]]
    events: List[Tuple[float, str]]

    def add_intervention(self, time: float, fn: Callable[[State], State]) -> None:
        """Schedule an intervention at specified time."""
        ...

    def get_state_at(self, time: float) -> State:
        """Get state at or before specified time."""
        ...

See Also