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.
  • Setup and run Jupyter server on HPC cluster.
  • Setup and run VS Code on HPC cluster.
  • A short VS Code tutorial.
• 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).
  • Singularity on Apple Silicon chips.

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

• Sun Grid Engine cluster for beginners, from MDC.
  • Commonly used commands.
• Use tmux to manage multiple interactive sessions.

Data access and sharing

• Download from dbGaP.

Software development tips

• Automatic package versioning in R for packages you develop.

Command line tools

• Monitor memory usage for a command line program.

AI tools

• Useful ChatGPT 4 prompts that we create and tested to work well in practice (2023).

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.

Misc.

• Python tips.
• R tips.
• Bash one-liner.
• Learn regular expression interactively.
• A list for effective computing, from Peter Carbonetto.
• An example R package (with Rcpp extensions), from Peter Carbonetto.