Short workshops: Current Topics in Bioinformatics

These workshops are free and open to all researchers at Harvard University and affiliated institutions.

  • Workshops on bioinformatics methods & related skills.
  • Once a month for 3 hours
  • Hands-on workshops - be prepared with your MAC or Windows computer
  • Free and open to everyone at Harvard University and its affiliates
  • Will typically meet the third Wednesday of the month from 1-4 online via Zoom (meeting time is subject to change-please check)
  • Sign up at the links below to receive the workshop Zoom link
Topic Pre-requisites Date/Time     Time             Registration        

Introduction to Shell                              

None 1/18/2023 1 - 4pm Closed

Intermediate Shell

Shell 2/15/2023 1 – 4pm Register!

Advanced Shell

Intermediate Shell 3/15/2023 1 – 4pm Register!

Git/Github

Shell 4/19/2023 1 – 4pm Coming soon

ML4Bio 

TBD TBD TBD Coming soon

Python basics

None 6/21/2023 1 – 4pm Coming soon

R basics

None 7/19/2023 1 – 4pm Coming soon

R Intermediate

R basics or 
Online R resource from Harvard Catalyst
8/16/2023 1 – 4pm Coming soon
Publication perfect I R basics or 
Online R resource from Harvard Catalyst
9/20/2023 1 – 4pm Coming soon
Publicaiton perfect II R basics or 
Online R resource from Harvard Catalyst
10/18/2023 1 – 4pm Coming soon

Rmarkdown/quarto

R basics or
Online R resource from Harvard Catalyst

11/15/2023 1 – 4pm Coming soon

Workshop descriptions (more coming soon):

Introduction to Shell: Many data analysis tools and computational resources require users to have a basic working knowledge of the command line interface (also referred to as UNIX, Linux, bash, shell). In this workshop participants will learn basic commands for navigating the file system, exploring file contents, and performing basic operations, such as moving, copying, and renaming files/folders. This workshop will get you started with the tools needed to use high performance computing (HPC) resources and handling your genomics data.

Intermediate Shell: The analysis of big data often require knowledge of the command line, and this workshop will build on the basic skills taught in the Introduction to Shell workshop to allow for greater automation. This workshop will include lessons on using the command-line text editor, Vim, to create and edit files, utilizing for-loops for automation, using variables to store information, and writing scripts to perform a series of commands in a sequential order.

Advanced Shell: Description coming soon 

Git/Github: In this workshop, we will explore using Git and Github as an easy way to track changes in documents over time, while facilitating collaboration with other team members. Together, Git and Github, allow for project development between multiple individuals while being able to retrieve all previous versions of the tracked documents. While initially designed for saving and developing code collaboratively, there are many advantages for using version control with Git and/or Github for other text files and substantial works such as articles, books, and dissertations. Also, since Github hosts the documents online, you never need to worry about losing your priceless work due to your computer crashing. Join us in the workshop to learn the simple bash commands needed to save versions of files on your local computer, as well as, how to make them accessible online on Github.

Basics of Python: Python is a powerful open source programming language. In this 3 hour, hands-on workshop, we will teach basic concepts and bioinformatics applications in Python. We will learn the Python syntax, data structures, functions, data manipulation, and data visualization. By the end of the workshop, students will understand and write simple Python scripts, and be able to perform basic data analysis in Python.

R Basics: R is a simple programming environment that enables the effective handling of data, while providing excellent graphical support. RStudio is a tool that provides a user-friendly environment for working with R. This workshop gives participants an overview of the basics of the R programming language and RStudio

Intermediate RThis workshop will build on the content of the Introduction to R online resource, or R Basics and will provide practical exercises to practice your newly developed R skills. Hands-on exercises will review learned R syntax, including variables, functions and arguments as well as data structures in R and the basics of data inspection and wrangling.

Generating reports with Rmarkdown: Reproducible research is as important for computational analysis as it is at the bench. Integrating your R data analyses into a report format allows for easy retrieval of the packages/versions and code used to generate your results and figures. It allows for efficient communication of your results with your collaborators. The knitr R package allows for the easy generation of professional reports for any R analysis, while allowing for customization and easy revision. In this 3-hour workshop, we will cover the simple RMarkdown syntax and explore options for customizing your reports.