SPAWN
Documentation

Model classes

A class describes the mechanics a specification must expose. It does not grant biological meaning or scientific validity.

[connectome-derived]

connectome-derived
Canonical equation
v_i(t+1) = (1 − 1/tau_m)v_i(t) + Σ_j W_ij s_j(t) + I_i(t) s_i(t+1) = [v_i(t+1) > theta_i]
Sourced data
Design choice
Published neuron identities, adjacency, synapse counts, and anatomical annotations.
Neuron dynamics, weights derived from counts, thresholds, delays, input mapping, and readout.

Typical S and c scale. S commonly grows with neurons plus edges; c ranges from moderate for sparse integer stepping to high for dense or conductance-based updates.

Datasets and references
  • 01FlyWire Consortium, adult Drosophila brain connectome — doi:10.1038/s41586-024-07558-y
  • 02Cook et al., whole-animal C. elegans connectomes — doi:10.1038/s41586-019-1352-7
Common overstatements rejected at the gate
  • 01“simulates a brain”
  • 02“the fly sees”
  • 03“reconstructs consciousness”

[reaction–diffusion]

reaction–diffusion
Canonical equation
∂u/∂t = D_u∇²u − uv² + F(1 − u) ∂v/∂t = D_v∇²v + uv² − (F + k)v
Sourced data
Design choice
A published equation, measured coefficients where available, and any empirical initial or boundary data.
Grid resolution, timestep, stencil, boundary conditions, parameters not taken from data, and visual mapping.

Typical S and c scale. S is species × grid cells; c scales with grid area, species count, stencil width, and arithmetic choice.

Datasets and references
  • 01Pearson, Complex patterns in a simple system — doi:10.1126/science.261.5118.189
  • 02Turing, The chemical basis of morphogenesis — doi:10.1098/rstb.1952.0012
Common overstatements rejected at the gate
  • 01“models real morphogenesis”
  • 02“recreates an embryo”
  • 03“proves a biological mechanism”

[coupled oscillators]

coupled oscillators
Canonical equation
dθ_i/dt = ω_i + (K/N) Σ_j A_ij sin(θ_j − θ_i)
Sourced data
Design choice
A published coupling graph, measured intrinsic frequencies, and recorded phase observations when present.
Coupling strength, integrator, timestep, initial phases, boundary behavior, and order-parameter readout.

Typical S and c scale. S is usually one or several values per oscillator; c is low for local sparse coupling and rises with dense all-to-all sums.

Datasets and references
  • 01Kuramoto, Self-entrainment of a population of coupled non-linear oscillators — doi:10.1007/BFb0013365
  • 02Strogatz, From Kuramoto to Crawford — doi:10.1016/S0167-2789(00)00094-4
Common overstatements rejected at the gate
  • 01“models the grid”
  • 02“models the brain”
  • 03“demonstrates neural synchrony in vivo”

[cellular automaton]

cellular automaton
Canonical equation
a_(t+1)(x) = R({ a_t(x + delta) : delta ∈ N })
Sourced data
Design choice
A published transition rule, neighbourhood, initial condition, or measured lattice when one is actually used.
Lattice dimensions, boundary conditions, update schedule, encoding, perturbations, and rendered interpretation.

Typical S and c scale. S is cell count × per-cell state; c is typically low for compact local integer rules and increases with continuous kernels.

Datasets and references
  • 01Chan, Lenia — Biology of Artificial Life — doi:10.25088/ComplexSystems.28.3.251
  • 02Wolfram, Statistical mechanics of cellular automata — doi:10.1103/RevModPhys.55.601
Common overstatements rejected at the gate
  • 01“is alive”
  • 02“evolves biologically”
  • 03“models a real organism”

[agent-based]

agent-based
Canonical equation
θ_i(t+1) = arg(Σ_{j: |x_j − x_i| < R} exp(iθ_j(t))) + η_i(t) x_i(t+1) = x_i(t) + v · [cos θ_i, sin θ_i]
Sourced data
Design choice
Measured trajectories, population counts, interaction ranges, or a published behavioural rule where available.
Agent policy, collision handling, noise process, environment, initial placement, and aggregate metrics.

Typical S and c scale. S grows with agents and their per-agent variables; c ranges from moderate with spatial indexing to high with all-pairs interaction.

Datasets and references
  • 01Vicsek et al., Novel type of phase transition in a system of self-driven particles — doi:10.1103/PhysRevLett.75.1226
  • 02Reynolds, Flocks, herds and schools — doi:10.1145/37401.37406
Common overstatements rejected at the gate
  • 01“predicts animal behaviour”
  • 02“models a real population”
  • 03“demonstrates collective intelligence”

Other classes are accepted when S, f, sigma, and tau are concrete and the provenance gate passes.