3 How to X
3.1 Get started
If you are new to computational biology and R programming, join the #bioinfo-primers
channel. Use the #help-x
channels to ask for help/answer others’ questions on R/Py programming, shell scripting, version controlling, or anything else that’s general and not project-specific. Use the corresponding #proj-x
channels for all project-related questions.
Check out the Slack tips in the pinned posts in #help-proj_management to get oriented since you are new to Slack (the channel used to be #howto-slack
)!
To re-familiarize yourself with R/Python/Unix, check out these two resources in addition to Slack | CompBio gists and R-Ladies East Lansing. If you are new to R-Ladies Aurora, R-Ladies East Lansing, and Women+ Data Science, check them out and join Meetup-RLA/Meetup-RLEL and their Discord/Slack to remain apprised of upcoming events and to connect with the local R and data science communities.
💡If you find other useful resources, please add them to this list (or share them with me).
3.2 Code
- Write, work with, and manage source code and data
- Prepare for and carry out code review
- Share data
- Write an R package
- DBMI software engineering team tips & tricks blog posts
3.2.1 Learn R
To learn R, I would recommend getting started with the pinned posts in #courses-primers.
A couple of helpful GitHub repositories - https://github.com/jananiravi/workshop-tidyverse (Intro to R's tidyverse package
— handy to learn right away) - Other R workshop materials from our R-Ladies East Lansing chapter: https://github.com/rladies-eastlansing - Interactive tutorials with learnr & swirl. - R for Genomics from Data Carpentry - R on HPC
- Coursera
- Intro to R programming and tidyverse
- Data visualization and Dashboarding with R specialization
- Getting Started with Data Visualization in R
- … and more | explore by topic, duration, skill-level
📌 Go-to books (also in pinned posts on Slack)
- R for Data Science (for tidyverse and such)
- Hands-On Programming with R (for base R) Intro to Git, GitHub resources
3.2.2 Intro to Machine Learning
- YouTube Videos
- Articles
- Coding Practice Sites
3.2.3 Learn Git/GitHub
- https://happygitwithr.com/ Happy Git and GitHub for the useR (connecting git/GitHub w/ R)
- Git and GitHub learning resources from GitHub
- Git 101
- Coursera Intro to Git and GitHub course
3.3 Access HPC, servers
For computing that requires high performance hardware and computing clusters, we utilize two different remote servers.
3.3.1 JRaviLab server
- A single high performance machine used only by our group.
- To request access, contact the system administrator
shaddai.amolitos@cuanschutz.edu
by sending him your CU username (e.g., the CU auto-generatedravijan
instead ofjanani.ravi@cuanschutz.edu
) and a brief message that you will need access to the server. CC janani.ravi@cuanschutz.edu, so they can both verify your access. - If you are new to remote server work, then it maybe helpful to learn about using an ssh config for managing your remote hosts.
3.3.2 Alpine HPC
- Alpine is the HPC cluster for all the University of Colorado campuses, including Anschutz.
- There is extensive documentation about getting setup
- At the moment, a web shell is the only access option for Anschutz members. This is different from a typical SSH login, and it is best to follow the official, latest Alpine documentation.
Whenever possible, we highly recommend using the VSCode extension which provides an IDE on the remote host without having to worry about server-side installation of other IDEs like RStudio or Jupyter.
3.3.3 Use VPN
3.4 Read/write/present
3.5 Plan your semester/year
Templates on yearly/semester planning and professional development are available here.