2015 Workshops

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 11    
         
Using Morpheus for matrix visualization and analysis
In this hands-on workshop, participants will learn to use Morpheus, a web-based application for matrix visualization and analysis. Participants will learn how to interact with multiple data types (e.g. gene expression and mutation in a heat-map-based view) and how to cluster, sort, and filter their data.
  April 28  
 
         
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    
         
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   Workshop Materials
         
Introduction to the Integrative Genomics Viewer (IGV)
In this workshop, participants will learn to use the Integrative Genomics Viewer (IGV), a popular desktop application for interactive visual exploration of a wide range of genomic data types. This is an introductory level workshop for those who have little or no experience with IGV. Topics include an overview of the IGV user interface and how to use the application to load and view data, with an emphasis on viewing different types of NGS data. The workshop will include both lecture and hands-on exercises.
  April 10    
         
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    
         
Best Practices for Variant Calling with the GATK
This workshop will focus on the core steps involved in calling variants with the Broad's Genome Analysis Toolkit, using the "Best Practices" developed by the GATK team. The GATK development team and invited guests will give talks explaining the rationale, theory and real-life applications of the Best Practices. You will learn why each step is essential to the calling process, what are the key operations 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. An optional hands-on session will be available to select participants. In this session, the GATK team will help beginners work through interactive exercises and tutorials to learn how to use GATK and apply the Best Practices to real data. 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 use 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 as regards the latest innovations.  
  March 19 & 20   Workshop Materials and Videos
         
Advances in Genome Engineering Using
CRISPR-Cas9

The rapid pace of advances in genome engineering technologies based on the CRISPR-Cas9 system is enabling a broad range of powerful and efficient methods to study biological systems. In this workshop, we describe recent advances in Cas9 technology for a variety of research or translational applications, and highlight challenges and important experimental considerations.
 
  March 11    
         
Microfluidics & Single Cell Genomics
This workshop will provide an overview of current techniques in microfluidics. We will cover:
  • Different modalities (glass, PC/PP/PE, paper and wax, PDMS)
  • PDMS as a biocompatible system
  • PDMS, with an emphasis on drops, pressure scaffold, and how to design your own device
We will also discuss where the technology is heading.
 
  February 23  
 
         
CURSOR Tool
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  
 
         
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    
         
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    
Genetic Perturbations for Functional Genomics
The Genetic Perturbation Platform workshop will explore functional genomics resources as the Broad, both for those interested in performing genetic screens and for those interested in using these tools to answer specific questions in their area of interest. The workshop is aimed at bench scientists who might use these resources as well as computationalists who want to understand more about biological mechanisms and experimental approaches underlying the data sets that emerge. We will cover the range of perturbations available in the Platform, including shRNAs, ORFs, and CRISPRs, including background on how they work and how they are delivered into cells. We will then discuss the planning and execution of small scale and genome-wide screens using these reagents. Additionally, we will provide hands-on examples of how to analyze and prioritize hits that emerge from screens, and discuss how to move from primary screening data to figures 3 through 7 of your publication.
  January 21   Workshop Materials