braingeneers

Runs spike sorting pipelines using the SpikeLab library (Kilosort2, Kilosort4, RT-Sort). Handles configuring and executing sorting jobs, curating units, inspecting and visualizing results. For stimulation experiments, runs artifact removal via…

Implements spike train data analysis and visualization using the SpikeLab library. Handles writing analysis and visualization scripts, managing results, and updating repo maps. Use when you want to load, analyze, or visualize spike train data with SpikeLab.

Integrates analysis code into the SpikeLab library. Takes user-provided scripts, identifies which computations already exist in the library, rewrites the script to use existing methods, integrates novel computations as new library methods, writes tests,…

Answers questions about SpikeLab analyses, neuroscience concepts, and how to interpret results. Read-only — never writes or executes code. Use when a user asks what an analysis does, how it works, what a result means, or wants to learn about the underlying…

Generates and updates the repo map files that document the SpikeLab library API. Run after installing or updating the library. Not intended for use during analysis sessions.

Design, deploy, operate, or diagnose Braingeneers services managed by mission_control on braingeneers.gi.ucsc.edu. Use for Compose service wiring, protected HTTPS API diagnosis, proxy and authentication patterns, shared infrastructure, secrets, packaging, and…

Run and analyze Braingeneers data-lifecycle two-run backup validation checks. Use when Codex needs to wait for an AWS Glacier inventory manifest, run the backup pipeline twice, compare artifacts/logs, detect steady-state reprocessing problems, investigate…

Build, deploy, and monitor Kubernetes batch jobs on the NRP Nautilus cluster. Use this skill for pipeline execution workflows, S3/W&B setup checks, jobs that call NRP-hosted open-weight LLMs or Brave Search through managed credentials, and job-level…

Sets up and manages the SpikeLab environment. Clones the repository, installs the library, generates repo maps, and delegates to in-repo skills for analysis, spike sorting, development, and education. Use when the user wants to work with SpikeLab.