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.

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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.

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Can I continue to use the Bash/RStudio environments we used in the workshop?

• 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

  How could I install this software on my workstation/laptop?

  • See Advanced setup instructions for details on how to install programs on your own computer.

Where can I learn more about Bash commands or RStudio functions?

• Bash cheatsheets:
  • https://files.fosswire.com/2007/08/fwunixref.pdf
• 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
• A nifty collection of cheatsheets for R and links to download some our favorites:
  • Base R - Data transformation with dplyr
  • Data visualization with ggplot2

Can you recommend other relevant workshops or turorials?

• The University of Michigan Bioinformatics Core hosts workshops through the year.
• Intro lessons and workshops in Bash / Git / R / Python :
  • Software Carpentry
  • 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.

How can I learn more about computational research at University of Michigan?

• UM CoderSpaces “office hours” and UM CoderSpaces Slack workspace. (See “Useful Resources” section in CoderSpaces page for instructions on how to join and access the CoderSpaces Slack workspace.)
• 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)

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Thank you

Thanks to/from the workshop team

Chris	Marci	Travis	Raymond
Dana	Matt	Nick

Thank you for participating in our workshop. We welcome your questions and feedback now and in the future.

Bioinformatics Workshop Team

bioinformatics-workshops@umich.edu
UM BRCF Bioinformatics Core