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BroadE Workshops

Demand for BroadE workshops is so high that they often fill quickly. To manage demand, we are continuing to increase the number of times we offer our workshops, and we have implemented a one-week registration period for all BroadE workshops. Participants are selected from the pool of applicants who register during this period.

Everyone who registers has an equal chance of being accepted. Registrants are given a priority number at random, and registrants with high priority numbers are put on a participant list. This list may be revised to ensure that BroadE workshops reach a diverse group of Broadies based on the following factors:

  • the applicant’s home institution
  • the applicant’s lab
  • whether the applicant has previously participated in this particular workshop
  • whether the applicant was previously waitlisted for this particular workshop
  • whether the applicant was previously selected to attend this particular workshop and failed to attend without notifying the BroadE organizers

We offer our most popular workshops several times throughout the year. If you are not selected to attend a workshop the first time you register, we encourage you to apply for a future session. 


Upcoming Workshops

Meta'omic Analyses for Microbial Communities
Microbial ecology is one of many fields that has benefited greatly from technical advances in DNA sequencing. In particular, low-cost, culture-independent sequencing has made metagenomic and metatranscriptomic (“meta’omic”) surveys of microbial communities practical, including bacteria, archaea, viruses, and fungi associated with the human body, other hosts, and the environment. The resulting data have stimulated the development of new computational approaches to meta’omic sequence analysis, including metagenomic assembly, microbial identification, strain tracking, and gene, transcript, and pathway functional profiling.


We will present a high-level introduction to computational meta’omics, highlighting the state-of-the-art in the field as well as outstanding challenges. This will include an introduction to the biological goals of typical meta’omic studies and the bioinformatic processes currently available to achieve them. 

Topics will include:

  • Reference genome-based community composition and functional profiling
  • Methods for constructing new genomic references by de novo assembly
  • The challenges associated with precisely quantifying members of a microbial community
  • Functional analysis of the gene families in a community
  • The association of gene families with their source organisms
  • The combination of gene families into pathways for metabolic profiling

We will conclude with an overview of the statistical challenges inherent to analyzing the compositional data arising in meta’omic studies.

Workshop attendees will gain hands-on experience with these analyses using bioBakery: a comprehensive platform for the analysis of shotgun meta’omic sequencing data. bioBakery includes tools for fast, accurate microbial taxonomic profiling (MetaPhlAn2), organism-specific functional profiling (HUMAnN2), identification/tracking of microbial strains (StrainPhlAn/PanPhlAn), and pattern discovery in microbial communities (MaAsLin, BAnOCC, and HAllA). Interspersed with lecture content, attendees will work through meta’omic analysis tutorials in Google Cloud instances of the bioBakery virtual machine.

This workshop will be run by members of the Huttenhower Lab of the Harvard T.H. Chan School of Public Health and Broad Institute

  November 1   Registration is closed
Best Practices for Variant Calling with the GATK
Workshop attendees will gain broad insight into the rationale of the GATK Best Practices for variant discovery, as well as a solid understanding of how individual GATK tools work and how to apply them in practice. Novices to the GATK will come out of the workshop knowing enough to identify which questions they can address using GATK tools, how to get started on designing their experiment and analytical workflow, and how to run the tools on their own computer. Existing GATK users will come out with a deeper understanding of how the GATK works under the hood and how to improve their results further, especially with respect to the latest innovations.

The workshop consists of an all-day lecture series and two optional hands-on tutorials on the second day.

Day 1: November 7 — Lecture
This workshop will focus on the core steps involved in calling variants with Broad's Genome Analysis Toolkit (GATK), using best practices developed by the GATK team. The GATK development team and invited guests will give talks explaining the rationale, theory, and real-world applications of the GATK Best Practices. You will learn why each step is essential to the variant-calling process, what key operations are performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset.

Special lecture topics include somatic variant calling with MuTect2 and somatic copy number variant calling.

Day 2: November 8  — Hands-on Tutorials

One of two optional hands-on tutorials will be available to select participants. In each tutorial, the GATK team will guide participants in applying GATK tools on provided example data. The two sessions reflect different stages of research — data generation and evaluation of results.

The morning session is titled Joint Variant Discovery, and participants will come out knowing how to use the GVCF workflow and how to interpret results. 

The afternoon session is titled Variant Callset Filtering and Evaluation, and participants will come out knowing how to use tools to evaluate and filter a variant callset.

  November 7-8   Registration is closed

Quantitative Proteomics in Biology, Chemistry and Medicine
The course will provide biologists, chemical biologists and clinicians with a working knowledge of the most relevant proteomic technologies and data analysis methods and will describe how these methods are being applied in a wide range of collaborative research at Broad.

  November 9   Registration is closed
CellProfiler: Learn to analyze 1 image or a 1,000,000
Microscopy and image processing methods improve every year. As the capacity to acquire and analyze images continues to grow, so too does CellProfiler, an open-source, freely-downloadable software designed for large-scale, automated phenotypic image analysis. Workshop attendees will learn the fundamentals of building CellProfiler pipelines to analyze image data, and will gain knowledge of the following:
  • Basics of image analysis.
  • Obtaining measurements from objects.
  • Basics of machine-learning for phenotype identification.

This hands-on introduction to CellProfiler will be followed by case-studies on HCS and cell-type classification. At the end of the workshop there will be a breakout session where attendees will receive guidance on analyzing their own image data. If you are curious about automating the analysis of your microscopy data or want to become familiar with "what's possible," come to the workshop and see what's new in CellProfiler for 2016.

  November 14   Register

Registration closes October 28 at 5 p.m.

In this workshop, we will briefly highlight some of the microfluidics projects taking place at the Broad. We will then introduce basic protocols and share information about the facilities and equipment available to researchers so that all attendees can determine how best to use microfluidics in their own projects. Anyone who is interested in using microfluidics for their research is encouraged to attend.
  November 22   Registration opens Monday, October 31

Registration closes November 4 at 5 p.m.

Primer on Medical and Population Genetics
The Primer on Medical and Population Genetics series includes informal discussions of basic topics relevant to medical and population genetics by speakers drawn from across the Broad community. The target audience includes technicians, grad students, postdocs, and established investigators just entering the field of complex trait genetics with the goal of bringing all up to speed on basic principles of human genetic variation, genotyping and sequencing methods, statistics, and analysis.

Please note: When the weekly MPG meeting is cancelled (due to weather, conflicting events, etc.), primers are also cancelled.

September - January

  No Registration Necessary