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 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   Registration is closed
Introduction to the Integrative Genomics Viewer (IGV)
In this course, participants will learn to use the Integrative Genomics Viewer (IGV) to view different types of genomic data. Topics covered include:
  • Overview of the IGV user interface
  • Viewing copy number data
  • Viewing DNA sequencing alignments, including single nucleotide variants and structural events
  • Viewing RNA-Seq data
  • Viewing ChIP-Seq data
  • Using IGV tools
The course will include both lecture and hands-on exercises.
  April 10   Registration is closed.
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   Registration is closed.
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 in many cases the molecular networks they integrate into remain obscure. This limits our progress towards biological insight and therapeutic intervention. Computational analyses that systematically integrate such lists with biological networks (e.g., protein-protein interactions) have emerged as a powerful approach to functionally interpret gene sets emerging from many different technological platforms.

This BroadE workshop will teach participants how to fully utilize the Broad Institute Web Platform for Genome Networks (GeNets), a new unified and flexible web app for analyzing, synthesizing, and visualizing gene sets using any biological network. At the end of the workshop, attendees will be able to conduct fast exploratory network analyses of their gene sets through the lens of several powerful networks (e.g., InWeb protein-protein interactions, CMap/LINCS connections, Achilles Cancer Co-dependencies, and gene-expression from Gene Expression Omnibus (GEO) and how to integrate their own data to find patterns and generate hypotheses. Furthermore, participants will know how to employ our pathway-learning algorithm to filter and segment their gene lists and predict new candidates.
  April 17   Registration is closed.
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