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Copyright (c) 2020+
Gao Wang and other lab members.
Distributed under CC BY-SA license.

Contents

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  • A (outdated) Debian / Ubuntu setup guide.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.
〈 Research resource This and that 〉