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2017 Workshops

Writing workflows in WDL and running them in FireCloud
This workshop will consist of two complementary sessions: one (morning) will focus on workflow-authoring with WDL, and the other (afternoon) will focus on executing those workflows on the FireCloud platform. The two sessions are independent of each other. (In other words, you can choose to attend one without having to attend the other.) Feel free to sign up for them separately, with the caveat that the FireCloud session will assume prior knowledge of WDL basics.

For more information on WDL, see https://software.broadinstitute.org/wdl/ For more information on FireCloud, see https://software.broadinstitute.org/firecloud/

Pre-requisites

Morning session: Participants should already be familiar with the basic terms and concepts of genetics and genomics, as well as the concept of analysis workflow. The WDL authoring session (morning) requires familiarity with the command line environment, basic usage of command line tools and basic scripting concepts.

Afternoon session: The FireCloud session (afternoon) does NOT require familiarity with command line or scripting concepts.

 
December 11
 
 
What's new in GATK4
This workshop will alternate between talks and practical exercises highlighting the key changes and updates in the new GATK version 4.0. We will cover the following topics:
  • Introduction to GATK4 + GATK Best Practices pipelines
  • Scaling germline variant discovery with GenomicsDB
  • Running Spark-capable tools on a Spark cluster (via Google Dataproc)
  • Calling somatic short variants with the new and improved Mutect2
  • Calling somatic copy number variants with GATK CNV

Participants will perform the exercises on their own laptops. Important note: Only MacOS and Linux systems are supported; MS Windows systems are NOT supported.

Please note that this workshop is focused on human data analysis. The majority of the materials presented do apply equally to non-human data, and we will address some questions regarding the necessary adaptations for such cases, but we will not cover much detail.

Prerequisites: Participants should already be familiar with the basic terms and concepts of genetics and genomics, including high-level understanding of high-throughput sequencing technologies and file formats used in genomic analysis. You should also be familiar with the command line environment and basic usage of command line tools. Familiarity with Spark and cloud computing concepts is NOT required.

 
December 5
 
Broad Cancer Data Resources & Tools 101
This introductory symposium aims to offer any interested scientist a chance to get an understanding of the landscape of some of the tools, datasets, and resources available for cancer research at the Broad including CCLE, Achilles, Firecloud, TCGA data, Copy Number Portal, GTEx, CMap, Gene Pattern, Morpheus, Tumor Portal, and more. Currently, these topics are only systemically discussed together in the ‘deep-dive’ format of the two-week long annual Cancer Program Postdoc BootCamp.

Therefore, this BroadE provides an exciting opportunity for people to learn more about how and why these resources and datasets may be applicable to their own research. The session may also provide introductory information about how to access or get assistance using these resources. Attendees do not need computational experience. Additionally, subsequent BroadE workshops are being planned that will explore and demonstrate these individual tools and datasets in greater detail through hands-on training.

  December 4
Bioimaging analysis: CellProfiler and beyond
Two major domains of high-content analysis techniques have remarkably advanced in the past couple of years:
  • Object identification
  • Quantity of features extracted per object

"Under the hood," both domains are being evolved by new computational tools — especially machine learning. In this light, the Imaging Platform at the Broad has pushed several efforts to implement these new advances into a user-friendly imaging analysis pipeline that is accessible for biologists.

In this workshop, participants will work through a series of hand-on experiments to learn:

  • How to use CellProfiler to extract information from microscopic images
  • How to use a combination of machine learning and CellProfiler to detect difficult objects better
  • How to move beyond just extracting information

We have many more to share!

The required software packages are CellProfiler and CellProfiler Analyst. For those who are interested in learning data mining beyond CellProfiler, please install R, devtools, and cytominer packages.

 

October 19

Navigating Genetic Screens with the GPP
This workshop hosted by the Genetic Perturbation Platform (GPP) will explore functional genomics resources at 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 collaborate with GPP to conduct a screen, as well as computationalists who want to understand more about the biological mechanisms and experimental approaches underlying the data sets that emerge. We will cover the range of perturbation technologies available in the Platform, including RNAi, ORF, and CRISPR. We will discuss the planning and execution of genome-wide and customized screens using these reagents, and then how to analyze the results. We will provide examples of success stories -- and cautionary tales -- and discuss how to move from primary screening data to figures 3 through 7 of your publication.
 

October 16

Video

CRISPR in a nutshell
  1. Introduction to CRISPR-Cas systems and basic genome editing methodologies (focusing on Cas9), including guide design, in vitro and in vivo delivery, and assaying results
  2. Guide to CRISPR-Cas9-based screening applications (both loss- and gain-of-function)
  3. Overview of frontiers in genome editing, including therapeutic delivery modes, approaches to enhancing specificity, and novel RNA-guided RNA-targeting enzymes

Each module will be followed by ample time for questions to ensure that participants get detailed advice tailored to their specific needs

 

September 18

Video

Introduction to Genoppi - Web application for interactive integration of experimental proteomics results with genetic datasets
In this workshop participants are introduced to Genoppi, an interactive and user-friendly app used to visualize proteomics results. We will cover how the app performs data quality control and clean up, as well as statistical analyses and integration with built-in and user-provided genetics data.
  June 30
Spectral Flow Cytometry
Day 1
Spectral Flow Cytometry is a new technology that encompasses both the high-throughput analysis of flow cytometry with the ability to measure the entire visible light spectrum of fluorescence on a single-cell basis by the use of prisms and PMT arrays. The morning session will highlight the advantages of spectral flow cytometry, how to design a smart panel for spectral flow cytometry, and the basics of acquisition and analysis. The afternoon session will dig into specific applications including a 7-color immuno-phenotyping panel, human T-regulatory cells, cell cycle, and fluorescent protein analysis.

Day 2
On the second day of the seminar we will be hosting one-on-one slots to talk about your own experiments and the design of your specific panel, or to get actual hands-on time with the facility's two spectral analyzers with your own cells or cells provided by the facility. The individual sessions will be limited. You will have the opportunity to sign up for a one-on-one slot during registration check-in on day one.

  April 25
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 12
The Broad Flow Cytometry Facility: Instrumentation, Applications, and Panel Design Tools
This workshop will highlight current instrumentation in the Broad Flow Cytometry Facility and what applications are ideal for each one. We will also go over online tools that are available for helping with panel design and how best to design your experiment for each instrument in the facility.
  April 7
MITE-Seq in a Nutshell
Historically, the ability to characterize all possible amino acid mutations in a gene of interest was a preposterous idea that would require armies of graduate students and postdocs. Today, this is no longer a dream: the creation of MITE-Seq has made saturation mutagenesis a reality.

In this workshop, we will discuss all aspects of the MITE-Seq approach, including assay design, library design, analysis and data visualization, additionally highlighting early use cases from the Broad community. Thinking about MITE? Then this course is for you!

  March 20
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.
  February 7
2016