Lab computational environment setup
- Columbia Neurology cloud HPC cluster documentation.
- Install JupyterLab with Script of Scripts suite.
- Connect from one computer to another: via JupterLab and VS Code.
- Singularity tips.
- Computing using AWS and MemVerge.
- Columbia Medical Center VPN.
- Columbia Medical Center Wifi.
- Computing FAQ from the lab.
MacOS setup
- A short note on setting up a new Mac OS for work (Last updated: 2023).
Linux setup
- An automated installation script written in SoS workflow (Last updated: 2022).
- Linux Mint setup (Last updated: 2020).
- Debian / Ubuntu setup (Last updated: 2015).
HPC reference
Data access and sharing
Software development tips
- Automatic package versioning in R for packages you develop.
Command line tools
AI tools
- Useful ChatGPT 4 prompts that we create and tested to work well in practice (2023).
- Using Claude on the HPC, an AI coding assistant with filesystem and terminal access, useful for HPC pipelines, SLURM jobs, and analysis notebooks (2025).
Other productivity tools
- obsidian, I find it useful for notes taking and outlining ideas.
- VS Code text editor for coding and writing Markdown files. It has Vim Keybinding extensions.
- Create multi-panel figures for quick presentation purposes.
Programming tips
Script of Scripts
- An SoS tutorial including how to submit SoS workflows on the Neurology HPC.
- SoS debug tips.
- Running SoS on HPC cluster resource allocation tips.