Wrapping up

We hope you now have more familiarity with key concepts, tools, and techniques that will enable more efficient, reproducible, and impactful computational research.

Housekeeping

Please take our optional post-workshop survey (5-10 minutes)
We will email you a link to the final session recordings by next week.
This workshop website will be available.
The UM Bioinformatics Core Workshop Slack channel will be available for 90 days.

Looking ahead

Workshop environment

BASH Shell and RStudio workshop compute environment will be available for one week from today.
- Please save all your R scripts now so that we can “right-size” the compute environment immediately following today’s workshop session.
You can download files from the workshop environment from your terminal/command line window as below. (You will need to substitute your actual workshop username and type workshop password when prompted.)
```
mkdir computational-foundations-workshop
scp -r YOUR_USERNAME@bfx-workshop01.med.umich.edu:"CF*" computational-foundations-workshop
```
Installing software locally
- See Advanced setup instructions for details on how to install programs on your own computer.

Continued training and support

Learning computational techniques is more like a process than a task. Resources to consider as you continues your study:

Some handy Bash cheatsheets:
- https://files.fosswire.com/2007/08/fwunixref.pdf
And a nifty collection of cheatsheets for R and links to download some our favorites:
ExplainShell.com can elaborate the flags of specific Bash commands:
Regular expression syntax (aka “regex”) is extremely powerful but also a broad topic unto itself
- Regex tutorial — A quick cheatsheet by examples
- A bit like ExplainShell above, but for regex expressions:
  https://regexr.com/
Intro lessons and workshops in Bash / Git / R / Python :
- Software Carpentry.

University of Michigan Resources

UM CoderSpaces “office hours” and UM CoderSpaces Slack workspace. (See “Useful Resources” section in above page for instructions on how to join and access the CoderSpaces Slack workspace.)
The Carpentries at the University of Michigan host several introductory workshops each year following curricula that are developed collaboratively and using the latest research into best practices for teaching computer science content. All workshops are offered for free to learners.
Upcoming UM Advanced Research Computing workshops.
Advanced Research Computing (ARC) at University of Michigan hosts a high-performance computing (HPC) platform called Great Lakes which combines high-end computers, fast/resilient storage, and pre-installed software. GreatLakes may be a good resource for folks who need to run the more compute intensive steps and a substantial block of compute and storage is subsidized by ARC making it essentially free to many researchers.
- About Great Lakes HPC.
- About the ARC Research Computing Package.
- Videos on getting started with Great Lakes. (available to UM folks)


Chris	Marci	Raymond	Travis


Dana	Irene	Sarah