Command-line reference

python -m neurogenesis

Command	Purpose	Key options
generate	preset network (column, layered, microcircuit)	--neurons --morphology --exc-ratio --pace-ratio --radius --height --layers --conduction-velocity --weight-scale --inh-scale --refractory --seed --out
simulate	run the integer reference kernel	--network --ticks --raster --seed
stats	topology and degree statistics	--network
export-presets	three preset networks for the viewer	--out-dir
estimate	memory and time per neuron model; with --project, of a development schedule stage by stage	--neurons --synapses-per-neuron --seconds --model (repeatable) --project --no-calibrate
fit	fit a Project’s Fit params to data targets (CMA-ES)	--project --targets --seeds --iterations --seed --out
validate	rerun a module’s validation assays (exit 1 on failure)	module.json --assays
install	install a module into the local catalogue	module.json --catalogue --force
modules	list installed modules	--catalogue
data info / data fetch	dataset size, license, citation; resumable, checksum-verified download	dataset --manifest --target --yes
profile check / profile show / profile report	check that every parameter of a profile has a status and a source (exit 1 on failure); list parameters with their status; what a project’s parameters rest on (metadata.profiles, genes, Fit)	profiles --all --online, project
ui-schema	export the versioned UI schema JSON for the desktop apps	--project --calibrated
export	write a network (JSON or NGB1) in another format; prints the export report	network --format {sonata} --out
import	read a network from another format into network JSON	path --format {sonata} --out

Every command has --help. Worked examples: Tutorial 1 — The command line.

python -m neurogenesis.bridge

JSON-lines server for apps and other programs. No options; see Bridge protocol, version 1.0.

Environment variables

Variable	Effect
JAX_PLATFORMS=cpu	force JAX onto the CPU
XLA_PYTHON_CLIENT_MEM_FRACTION	fraction of GPU memory JAX may take
NEUROGENESIS_CACHE	calibration cache directory (default ~/.cache/neurogenesis)
NEUROGENESIS_MODULES	module catalogue directory (default ~/.cache/neurogenesis/modules)
NEUROGENESIS_DATA, NEUROGENESIS_DATASETS	dataset cache; extra manifest directory
NEUROGENESIS_PROFILES	pharmacology profile directory

PLACEHOLDER

Planned: neurogenesis run, neurogenesis stages --json, neurogenesis data list.