2015 Workshops

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
Advances in Genome Engineering Using

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 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