How Biosimulant Works

Biosimulant is an open-source Python engine for composing biological simulators and finite computations from modules with explicit typed ports. BioWorld drains before/after computation and advances temporal modules through atomic communication windows.

If you want a runnable introduction, start with the Library Quickstart (Python). This page explains the architecture behind that example.

The five core primitives

BioWorld: communication windows

Create a world with a required communication step:

world = biosim.BioWorld(communication_step=0.1)

ONCE_BEFORE_RUN modules run first, in dependency order. Then, for each window [t, t + communication_step]:

1. the world reads committed signals at t
2. it delivers those inputs to every connected target module
3. every EACH_WINDOW module advances or executes across the same positive window
4. the world commits all outputs atomically at t + communication_step

After the final window commits, ONCE_AFTER_RUN modules run in dependency order.

This means:

• signal exchange is synchronized at shared communication boundaries
• state signals use hold-last-value semantics until replaced
• event signals are delivered once per connection per source timestamp
• stale reads are checked from the consuming port’s SignalSpec

The kernel does not expose an execution-order scheduling contract, a global external tick parameter, rollback, or algebraic-loop solving.

A module sees another module’s output on the communication turn after it is committed. Final outputs are committed at the last boundary, so a downstream module that needs them should use ONCE_AFTER_RUN. Older temporal modules that implement advance_window() can use settle_steps / world.settle() instead.