Testing developmental hypotheses

Because development is explicit and seeded, one can ask “what if” questions and test them across many developmental seeds:

Manipulation	How
Remove a cell population or a projection	knockout(genome, regions=[...], projections=[...])
Remove a guidance cue	delete or neutralise its gene; rules are inactive without their genes
Change the timing of a stage	reorder the schedule, change repeat or when
Block spontaneous activity	remove or silence the refine_by_activity stage
Change a cell type’s resting state	genome["tonic"][region] (standing currents)
Change transmitter polarity during development	planned (phase P: stage-dependent pharmacology)

A list of well-characterised developmental steps, with the questions the toolbox could address, is in Developmental Neuroscience Questions for Circuit Modeling.

Results are statements about the simulation: “in this simulation, removing X abolishes Y across 95 / 100 seeds”, not claims about the animal.

PLACEHOLDER

A worked knockout study on the topographic-map example (which genes are necessary for topography, measured across held-out seeds), with figures.