The Current Topics in Bioinformatics 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 above to receive the workshop Zoom link

Spring 2024 schedule - Big data? Big computer! The skill set you need to succeed:

* Please note: the June workshop is moved to the 4th Wednesday of the month due to the Juneteenth holiday.

The Spring 2024 Workshop Series is: Big data? Big computer! The skill set you need to succeed.

As genomic data accumulates at astronomical rates, biology has evolved into a “big data” science. To meet this challenge, we need to use high performance computers that are hundreds of times more powerful than our laptops.

Join the Harvard Chan Bioinformatics Core for a workshop series designed to empower you with the essential skills for using high performance computers (HPC) to analyze complex data!

Whether you're a bioinformatics beginner or simply looking to enhance your data science skills for real-world applications, this series will increase ability to use HPCs effectively. We start by demystifying the command-line interface and then equip you with the tools and knowledge you need to tackle big data analyses in an efficient manner. 

Workshop descriptions:

The Foundation - Basic Shell: Bioinformatics requires computational resources that go beyond what your laptop has available. To access high performance computing (HPC ) resources, users need to have a basic working knowledge of the command line interface (CLI - also referred to as UNIX, 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 module is a pre-requirement for all other Spring 2024 modules. 

Accelerate with Automation - Making your code work for you: This intermediate shell workshop builds upon the basic shell skills learned in The Foundation - Basic Shell. In this workshop, participants will learn how to write basic shell scripts and how to enhance the automation of those scripts through the implementation of loops as well as the incorporation of positional parameters. Participants will also be introduced to slurm arrays and their utility on a high performance cluster.

Needle in a Haystack - Finding and summarizing data from colossal files: Manipulating large files in a compute cluster environment (such as HMSRC's O2 cluster) is a key bioinformatics skill. In this workshop we introduce participants to a handful of command-line utilities for data wrangling in shell. Participants will learn to grab information with ‘grep’ and use regular expressions to widen their searches. Then we will get into more complex file manipulations and data summarizing with sed and awk. This intermediate shell workshop builds upon the basic shell skills learned in The Foundation - Basic Shell. This workshop will not be taught on the O2 cluster, rather commands will be demonstrated in a local laptop setting.

Shell Tips and Tricks on O2: In this workshop we invite users of the HMS Research Computing Cluster O2 and members of the Harvard community who are interested in using a compute cluster to join us as we demonstrate some very helpful tips and best practices. We will introduce participants to various commands and approaches to help effectively navigate use the cluster and complete tasks in an efficient manner. We encourage participants to log on to the cluster and follow along interactively, however attendees can also watch the demonstration. This workshop is being held in collaboration with HMS Research Computing, and is an advanced workshop requiring knowledge of the command-line and/or the basic shell skills learned in The Foundation - Basic Shell.

R Basics: This workshop will give participants an overview of the basics of R and RStudio. 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 module is a pre-requirement for the upcoming Publication Perfect I and II modules.