Center for Public Health Genomics Computation Group

A portal to welcome new programmers to CPHG at UVa

Welcome

Welcome to the CPHG Computation Community! This webpage and associated repository is meant to serve as a community-curated portal to the many valuable people and resources you will work with as a member of the CPHG computational community. Please feel free to submit issues to this site and contribute to the resources listed here. Welcome to CPHG Computing!

Contents

• Meetings
• CPHG
• CADRE
• ARCS
• SOMRC
• Databio
• Affiliated Resources
• Unaffiliated Resources
• Command Line Tools
• Text Editors
• Configurations
• GitHub
• CPHG IT Infrastructure

Meetings

We meet in-person, as a group, once every few weeks to discuss topics of interest to community members. Vote on the next topic here: Google Docs link

CPHG

• Homepage
• UVaCollab page
  • Richard or someone else with access to this page, please add full URL
• Github site for trainees
  • This site does not appear to have been developed much

UVa Computation and Data Resource Exchange (CADRE)

• CADRE is a University-wide exchange designed to simplify the process of finding local research technology solutions. The CADRE website provides a comprehensive list of the software, services, training opportunities, storage solutions, and computational hardware available to UVa scholars.
• CADRE organizational chart

UVa Advanced Research Computing (ARCS)

• Homepage
• Rivanna
  • Rivanna is UVa's High-Performance Computing (HPC) system. Rivanna is open to all faculty, research staff, and graduate students of the University.
• Rivanna status page
• ARCS SLURM page
• ARCS Getting Started page
• ARCS Storage page
• ARCS File Transfer tools
• ARCS Globus page

UVa School of Medicine Research Computing (SOMRC)

• Homepage, on github, and on dockerhub
• Ivy
  • Ivy is a secure computing environment for researchers working with sensitive data. The environment meets HIPAA requirements. Access to Ivy resources is project-based, limited to PIs and their designees, and requires approval. HPC services will be coming soon to the Ivy environment.
• SOMRC Globus page

Databio Bioinformatics Skills Resources

• Nathan Sheffield curates a list of resources to help students interested in developing foundational skills useful for computational biology on his website.

Affiliated UVa Resources

• UVa Computational Biology Slack channel
• UVa Biomedical Data Sciences Hackathon

Unaffiliated Resources

• Shirley Liu's Bioinformatics and Computational Biology course page

Command Line Tools

• Some basic utilities (mostly for macOS)
  • iTerm2
  • XQuartz
  • osxfuse
  • Globus CLI
• Unix/Linux Tutorials
  • ARCS Unix tutorial
  • An informal discussion of aliases vs functions vs scripts
• Getting Started
  • Unix commands for your first day
  • Python on Rivanna
• Group member favorite commands
  • Chris Dampier
  • Next Member

Text Editors

• Atom
• Nano
• Emacs
• Sublime
• Vim
• Visual Studio Code

Configurations

.bash_profile and .bashrc files

• How-to guide for building your own .bashrc file
• Example of a popular .bash_profile to give you some ideas
• Group member bash configurations
  • Chris Dampier
  • Cassie
  • Your Name

Modules

• ARCS LMod page
• LMod documentation

Containers

• Containerd homepage and on github
• Docker homepage and Docker hub

Virtual Machines

• SOMRC VMs

GitHub

• Homepage
• Karl Broman's minimal Github tutorial
• Nathan Sheffield's conceptual introduction to github

CPHG IT Infrastructure

• We would like to make the CPHG server structure explicit to all CPHG members, but it seems we need to put such a resource behind a firewall and require NetBadge login for security. I haven't learned the best way to do that yet.
  • Maybe a collab site
  • Key directories with useful resources available on the servers:
    • $HOME/apps : contains shared installation of commonly used tools including perl, python, R and SAS
    • $HOME/apps/statgen : contains a variety of widely used statistical genetics packages
    • $HOME/eQTL-Omics-PublicData : contains a variety of publicly available eQTL resources
    • $HOME : contains a variety of public resources
    • Note: for security reasons, I have not written the location of "$HOME" here. Please check with fellow members of CPHG to find out the location of $HOME.

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CPHG Computation Group