Lab computational environment setup

• Columbia Neurology HPC cluster guide (private document).
• Install SoS with JupyterLab and Docker.
  • An SoS tutorial including how to submit SoS workflows on the Neurology HPC.
• Connect from one computer to another: via JupterLab and via shell.
  • Setup and run Jupyter server on cluster.
• Singularity tips.
• SoS debug tips.
• Columbia Medical Center VPN.
• Columbia Medical Center Wifi.
• Computing FAQ from the lab.

Linux OS setup

• Linux Mint setup.
• An automated installation script written in SoS workflow.
• A (outdated) Debian / Ubuntu setup guide.

HPC computing

• Sun Grid Engine cluster for beginners, from MDC.
• Commonly used commands on HPC cluster.

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.

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.

Programming tips

• 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.