stanislavjiricek/phase-brain-run
skills/phase-brain-run/SKILL.md
Phase guidance for the neuroflow /brain-run command. Loaded automatically when /brain-run is invoked to orient agent behavior, relevant skills, and workflow hints for running brain model simulations.
$ install --global
skillsauthnpx skillsauth add stanislavjiricek/neuroflow phase-brain-runInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- phase-brain-run
- description:
- Phase guidance for the neuroflow /brain-run command. Loaded automatically when /brain-run is invoked to orient agent behavior, relevant skills, and workflow hints for running brain model simulations.
phase-brain-run
The brain-run phase covers configuring and executing a simulation run — setting duration, time step, inputs, and recording targets, then collecting and sanity-checking outputs.
Approach
- Locate the model code from
.neuroflow/brain-build/before configuring a run - Write
run-config.mdfirst — make run parameters explicit and reproducible - Sanity-check outputs immediately after the run: look for no-spike silence, runaway activity, NaN values, or implausible rates before storing results
- Keep run configs versioned in
.neuroflow/brain-run/so runs are reproducible
Relevant skills
neuroflow:neuroflow-core— read first; defines the command lifecycle and.neuroflow/write rules
Workflow hints
- All simulation output files (spike data, voltage traces, figures) go to
output_path(models/results/), not inside.neuroflow/ - Save
run-config.mdandrun-summary.mdto.neuroflow/brain-run/ - Note any run that produces qualitatively new or unexpected behaviour in
.neuroflow/reasoning/brain-run.json - For HPC submission: produce a job script (SLURM/PBS) alongside
run_sim.pyand save both tooutput_path
Slash command
/neuroflow:brain-run — runs this workflow as a slash command.
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