Training

With funding from the HMS Tools and Technology Committee, the Harvard NeuroDiscovery Center (HNDC) and the Harvard Stem Cell Institute (HSCI) we have a dedicated bioinformatics training program for:

  • HMS researchers with a primary affiliation in one of the Basic and Social Science Departments on the Quad
  • researchers with an affiliation with the HNDC
  • HSCI researchers

In addition, we also teach short courses for Harvard Catalyst.


Upcoming workshops/courses:

Please find a list of our various offerings below categorized by eligibility. If you would like to receive emails from us about training opportunities, please fill out this form.

For HSCI, HNDC and on-quad HMS researchers

  • February 26th - 28th, 2018: Introduction to R: Basics, Plots, and RNA-seq Differential Expression Analysis. Registration is now closed.

  • March 21st - 23rd, 2018: Introduction to ChIP-seq using high-performance computing. Registration will open pn March 1st, 2018.

Harvard Catalyst Workshops

  • April 5th, 6th, 12th and 13th, 2018: Introduction to R: Basics, Plots, and RNA-seq Differential Expression Analysis Apply for this workshop here!

For all researchers at Harvard University and affiliated institutions

We are excited to announce a new set of workshops for Spring 2018 in the Current Topics in Bioinformatics series of short workshops.

Similar to last semester, each of these 2 to 3 hour, hands-on workshops are freestanding, but some of them will have prerequisites. They will be held monthly in the Longwood Medical Area at either HSPH or HMS. The workshops are first-come-first-served and there is no registration process, so we encourage you to be punctual!

Please bring a laptop to be able to follow along in class. For instructions to prepare yourself and your laptop for the workshop, please click on the link to the workshop you are interested in attending in the table below.

Spring 2018 schedule and lesson links:

Lessons Date Timing Location Prerequisites
Introduction to the command-line interface 1/26/2018 1-4pm HSPH, Building Kresge, Room G2 None
Intermediate bash 2/23/2018 1-4pm HSPH, Building Kresge, Room G2 Beginner bash or Intro to the command-line interface
Version control using Git and Github 3/13/2018 1-4pm HMS-TMEC, Room 227 Beginner bash or Intro to the command-line interface
Accessing genomic reference and experimental sequencing data 4/27/2018 1-4pm HSPH, Buliding FXB, Room G12 Beginner bash or Intro to the command-line interface
Exploring genomic variants using the GEMINI framework 5/25/2018 1-4pm HSPH, Buliding Kresge, Room 502 Beginner bash or Intro to the command-line interface

Training program description:

We provide bioinformatics training through both shorter workshops and in-depth courses. [Click here for a list of upcoming workshops/courses]

1. Workshops

  • Next Generation Sequencing Introduction Series

    (Galaxy-based) workshops on RNA-Seq, ChIP-Seq to introduce basic concepts of Next-Generation Sequencing (NGS) analysis. The goal of these workshops are to enable researchers to design their studies appropriately and perform preliminary data analyses.

  • Basic Bioinformatics Skills Series

    Topics include R, data visualization using R, Python programming, Unix and high-performance computing (duration varies from half a day to three days).

2. In-Depth Next Generation Sequencing Analysis Courses

These intensive courses run for 10-12 days and are aimed at bench biologists interested in learning how to perform independent, best practice NGS-based analyses. Topics include:

  • Unix & High-Performance Computing (Orchestra)
  • NGS data analysis (RNA-Seq, ChIP-Seq, Variant calling)
  • Statistical analysis using R
  • Functional analysis

No prior NGS or command line expertise is required for our workshops or courses unless explicitly stated.


Past Workshops:

2018

  • [HSCI/TnT] January 29th - 31st: Introduction to RNA-seq using high-performance computing

2017

  • [HSCI/TnT/HNDC] December 6th & 7th: Introduction to R
  • [HSCI/TnT/HNDC] November 20th & 21st: Introduction to RNA-seq using high-performance computing
  • [Harvard Catalyst] November 1st - 3rd: Introduction to R and Differential Gene Expression (DGE) analysis for RNA-seq
  • [HSCI/TnT/HNDC] October 25th & 26th: Using DESeq2 for Differential Gene Expression
  • [Harvard Catalyst] September 25th - 27th: Introduction to RNA-seq using high-performance computing
  • [HSCI/TnT/HNDC] September 13th & 14th: Introduction to R
  • [HSCI/TnT/HNDC] August 23rd & 24th: Introduction to RNA-seq using high-performance computing
  • [HSCI/TnT/HNDC] May 31st - July 7th: In-depth NGS data analysis course
  • [Harvard Catalyst] May 17th - 19th: Introduction to R and Differential Gene Expression (DGE) analysis for RNA-seq
  • [HNDC] April 20th: Introduction to R
  • [HSCI/TnT/HNDC] April 3rd & 4th: Introduction to R
  • [Harvard Catalyst] March 16th: Introduction to RNA-seq with Galaxy
  • [HSCI] March 6th & 7th: Introduction to UNIX and Orchestra with HMS-RC
  • [HSCI/TnT/HNDC] February 15th: Introduction to Differential Gene Expression (DGE) analysis for RNA-seq
  • [TnT/HNDC] February 10th & 13th: Introduction to R
  • [HSCI] January 24th & 25th: Introduction to R

2016

  • [Harvard Catalyst] November 17th & 18th: Introduction to UNIX and Orchestra with HMS-RC
  • [HSCI/TnT/HNDC] October 31st - December 2nd: In-depth NGS data analysis course (RNA-Seq)
  • [HSCI/TnT/HNDC] October 20th: Introduction to Differential Gene Expression (DGE) analysis for RNA-seq
  • [Harvard Catalyst] October 14th: Introduction to RNA-seq with Galaxy
  • [TnT/HNDC] September 29th & 30th: Introduction to R
  • [HSCI] September 8th & 9th: Introduction to R
  • [HSCI] August 22nd & 23rd: Introduction to UNIX and Orchestra with HMS-RC
  • [HSCI/TnT/HNDC] June 22nd - August 12th: In-depth NGS data analysis course
  • [HSCI] May 23rd & 24th: Introduction to UNIX and Orchestra with HMS-RC
  • [TnT/HNDC] May 12th & 12th: Introduction to UNIX and Orchestra with HMS-RC
  • [HSCI/TnT/HNDC] February 8th - March 8th: In-depth NGS data analysis course

2015

  • [HSCI] December 11th: Introduction to R
  • [TnT/HNDC] November 23rd: Introduction to RNA-seq with Galaxy
  • [HSCI] November 13th: Introduction to RNA-seq with Galaxy
  • [TnT/HNDC] October 8th & 9th: Introduction to UNIX and Orchestra with HMS-RC
  • [TnT/HNDC] October 2nd: Introduction to RNA-seq with Galaxy
  • [TnT/HNDC] September 21st: Introduction to RNA-seq with Galaxy
  • [TnT/HNDC] September 11th: ChIP-Seq with Galaxy
  • [TnT/HNDC] August 14th: Introduction to RNA-seq with Galaxy
  • [TnT/HNDC] July 22nd: A Hands-on Introduction to Python (in collaboration with IQSS)
  • [TnT/HNDC] July 17th: Introduction to RNA-seq with Galaxy
  • [TnT/HNDC] June 26th: Introduction to R and R graphics with ggplot2 (in collaboration with IQSS)

Contact:

For any training-related questions, please email us at hbctraining@hsph.harvard.edu.

Training materials can be accessed here. Please read our licensing information prior to reusing or adapting our materials.