Broad Workshops

BroadE workshops bring researchers in the extended Broad community together so they can learn from one another. BroadE workshops (the 'E' stands for education) offer insights and share hands-on training in breakthrough technologies, high-throughput methods, and computational tools not typically found in conventional research labs. Through this ongoing series, which is open to Broad staff and to researchers at MIT, Harvard and Harvard-affiliated hospitals, the Broad community hopes to extend the impact of its science and openly share new methods.


New Registration System

It’s official — BroadE is a rousing success! In fact, demand is so high that our workshops quickly reach capacity, sometimes only minutes after being posted.

To meet this overwhelming demand and promote access to all in our community, we will repeat our most popular workshops during the coming year.

In addition, we will implement a new registration system for BroadE workshops occurring in June 2013 and later. Going forward, when a BroadE workshop is announced, we will also open a one-week application period. Participants will be selected from the pool of applicants who register during this period. In selecting participants from this pool, we will consider:

  • the applicant’s home institution
  • the applicant’s lab
  • whether the applicant has participated in previous workshops

This new registration practice will help us to ensure that BroadE workshops reach a diverse, balanced group of Broadies.


Upcoming Workshops

Using GeNets for Network Based Analyses of Genomic & Proteomic Data
The recent advances in genomics and proteomics have produced many lists of genes and proteins likely to be involved in disease processes, but the molecular networks they integrate into remain obscure in many cases. This limits our progress towards biological insight and therapeutic intervention. Computational analyses that systematically integrate such lists with biological networks (i.e., networks in which genes are connected if they are functionally associated in transcriptional, protein-protein interaction, phylogenetic or text mining data) have emerged as a powerful approach to functionally interpret gene sets emerging from many different technological platforms.

This BroadE workshop will introduce the audience to the Broad Institute web platform for Genome Networks - GeNets - a new unified and flexible web platform for analyzing, integrating, and visualizing gene sets using any biological network. Through GeNets, users can easily share interactive network analyses with collaborators and obtain publication-grade figures of the results.
  January 30   Registration is closed
Integrative Genomics Analysis with GenomeSpace
This workshop will focus on integrative genomics analysis with GenomeSpace, an environment that brings together a diverse set of computational tools, enabling nonprogramming scientists to easily combine the tools’ capabilities through a user-friendly point-and-click interface. It offers a common space to create, manipulate, and share an ever-growing range of genomic visualizations and analyses.

GenomeSpace features support for cloud-based data storage and analysis, multi-tool analyses, automatic conversion of data formats, and ease of connecting new tools to the environment. A set of six “GenomeSpace-enabled” seed tools developed by collaborating organizations provides a comprehensive platform for the analysis of genome data: Cytoscape, Galaxy, GenePattern, Genomica, Integrative Genomics Viewer, and the UCSC Genome Browser. The extensible format of the system has empowered a wider range of analyses through the continual addition of new tools and resources.

Participants in this workshop will learn how to use GenomeSpace to utilize the visualization and analysis capabilities of multiple tools in several research scenarios. Through the demonstration of a number of short analysis “recipes,” we will give participants the essential elements to construct powerful integrative genetic and genomic analyses.
  February 5   Registration is closed
CURSOR is a new way to look at genomic data that breaks away from the traditional linear displays. It focuses on regions of enrichment, and may be characterized as a "peaks explorer." After loading multiple tracks to CURSOR, the user selects one track's features as anchors — the base set of regions that are displayed. These regions can then be further filtered or sorted in a data-driven manner. Quick succession of selecting an initial set of regions, filtering, and sorting allows efficient visual exploration of many relations between data sets. In addition, CURSOR is designed to display any set of coordinate-based features, and can be used to integrate data of multiple diverse sources and types. CURSOR is very easy to use, but it helps if someone shows you the basic tricks. In the tutorial, you will learn how to load data to CURSOR and manipulate its display, as well as demonstrate how to work with session files.
  February 12   Register

Registration closes Friday, January 23 at 5:00 pm
Microfluidics & Singe Cell Genomics   February 23    
GATK   March 19 & 20    
Using CellProfiler for Biological Image Analysis
This workshop will instruct participants in the use of CellProfiler, an open-source, freely-downloadable software package designed for large-scale, automated phenotypic image analysis. Attendees are encouraged to contribute sample images from their assays as part of the demonstration. We will also briefly discuss the basic principles of supervised machine learning in order to score phenotypes where phenotypic differences between samples are not visible by eye.
  March 30    
Strategies for Visualizing Data
Data visualization is becoming increasingly important in biomedical research as a means to explore data for patterns and relationships. Such exploration, driven by the graphical representation of information, is the critical first step to inform subsequent computational and machine-driven approaches to data analysis. The process requires us to further define clear objectives and improved implementation to be successful. Data for the most part have no natural form or “look” - we have to make choices about how they are displayed. Each decision can bring out certain kinds of patterns in data while hiding others. We rely heavily on our intuition, common sense, and precedent in published material when we visually depict data. This is largely an unscientific process. In this workshop we will explore systematic approaches that rely on core graphic design principles and vision science (i.e. how we decode information encoded in graphical form) to develop effective visualizations of data.
  April 15    
Gene-E Tool   April 28    
Everything you always wanted to know about Proteomics but were afraid to ask
This half-day course will present essential aspects of proteomics of general interest to biologists and clinicians. Attendees will come away with a strong understanding of the important technologies and experimental approaches used in modern mass spectrometry-based proteomics.
Topics and applications presented will include:
  • Key types of proteomics experiments and sample requirements 
  • Quantitative MS approaches for global proteome and posttranslational analyses 
  • Basics of targeted MS for precise, reproducible measurements of peptides, proteins and their modifications in biology and medicine 
  • Data analysis approaches and statistical methods for confident identification of true differential proteins/peptides
  • Useful tools for annotating the MS results and to extract knowledge and organize results into pathways presented.
  May 8    
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