2019 Workshops

An Introduction to Image Analysis with CellProfiler
Microscopy and image processing methods improve every year. As the capacity to acquire and analyze images continues to grow, so too does CellProfiler, an open-source, freely-downloadable software designed for large-scale, automated phenotypic image analysis. Attendees will have a hands-on introduction to CellProfiler and ilastik, followed by case-studies on HCS and cell-type classification.

Editing the genome with prime and base editors
The development of programmable genome editing tools that can efficiently modify DNA sequences inside of living cells has transformed the life sciences. During this workshop, we will explore and summarize the current suite of available genome editing methods, paying particular attention to precision editing technologies established in the Liu laboratory. In 2016, the Liu laboratory reported their first programmable C-to-T base editor (CBE), which enables the precise introduction of C:G to T:A base pair transition mutations at targeted positions in the genomes of mammalian cells. Since this time, an A-to-G base editor (ABE) and several variant constructs have been developed. Last month, the Liu laboratory described an entirely new genome editing method known as prime editing. Prime editing vastly expands the versatility of potential edits, but comes with a unique set of design challenges. After an introductory overview, we will present the state-of-the-art in prime and base editing and discuss considerations for choosing a particular editor and guide RNA spacer based on the target sequence's features. Case examples will be covered during the lecture, and participants are encouraged to email the instructors a week or more in advance of the workshop with target mutations of interest.

NMR spectroscopy to study biomolecular structure and dynamics
This seminar will be designed for researchers in the Broad community to understand the variety of tools that could be useful to address challenges in our research. Starting with the background and key concepts of how NMR experiments work, we will discuss how various molecules can be quantitated and structurally characterized. Key applications are in the elucidation of small molecule structure, protein-ligand interactions, and the determination of three-dimensional structures of small proteins and their dynamics.

How to work and collaborate easily and securely on the cloud with Terra
This workshop will get you up and running with Terra, the new scalable platform for biomedical research developed at the Broad Institute in collaboration with Verily Life Sciences. (If you’ve seen or used FireCloud, think of Terra as the new and improved user interface that makes doing research easier than before!).

We will first cover the basics of doing research on the cloud and introduce you to Terra and the Data Biosphere. You’ll then get hands-on with Terra, learning how to access research data, run analysis tools, and seamlessly collaborate, all in a secure and scalable environment. We will guide you through running example workflows, interacting with Jupyter Notebooks, and working with the BigQuery data warehouse to help accelerate your own project in Terra. We will also show you how to manage data, security, and billing in Terra so that you can relax and focus on your science.

Target audience: Researchers new to cloud computing, FireCloud users, and project managers interested in learning how to use Terra.

We will first cover the basics of doing research on the cloud and introduce you to Terra and the Data Biosphere.  You’ll then get hands-on with Terra, learning how to access research data, run analysis tools, and seamlessly collaborate, all in a secure and scalable environment. We will guide you through running example workflows, interacting with Jupyter Notebooks, and working with the BigQuery data warehouse to help accelerate your own project in Terra.  We will also show you how to manage data, security, and billing in Terra so that you can relax and focus on your science. 

Target audience: Researchers new to cloud computing, FireCloud users, and project managers interested in learning how to use Terra.

The ENCODE project is building a comprehensive parts list of functional elements in the human genome, and mapping the regulatory mechanisms that control gene expression. ENCODE consists of ~15,000 curated  datasets, and continues to grow.

In this workshop, you’ll learn how to search, analyze, and visualize ENCODE data. First, leaders from the ENCODE data coordination center at Stanford (DCC), and data analysis center at UMASS (DAC) will teach you how to access and work with data via both the ENCODE portal and SCREEN. Second, Noam and Sushma from Broad Epigenomics and the DSP Terra team will teach you how to access and analyze ENCODE data in the cloud, via both the ENCODE Data Coordination Center (DCC)/AWS and Terra/Google Cloud. Finally, you’ll learn from Neva in the Aiden lab how to identify and visualize 3D genome interactions using ENCODE data in Juicebox. Representatives from the ENCODE DCC will also be on hand all day to answer your questions and help troubleshoot. This will be a hands on workshop, but no prior experience is necessary as there will be demos and experts on hand to teach at different levels. This is a whole-day workshop, lunch will be provided.

Best Practices for Variant Calling with the Genome Analysis Toolkit
The workshop focuses on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit (GATK), using the “Best Practices” developed by the GATK team. Participants will learn why each step is essential to the variant discovery process, what are the 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 their dataset.

This workshop focuses on calling germline short variants and somatic short variants and copy number alterations with Broad's Genome Analysis Toolkit (GATK), using best practices developed by the DSP Methods development team, who develop GATK. The developers will give talks explaining the rationale, theory, and real-world applications of the GATK Best Practices. You'll learn why each step is essential to the variant-calling process, what key operations are 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. If you're an experienced GATK user, you'll gain a deeper understanding of how the GATK works under the hood and how to improve your results further, especially with respect to the latest innovations. The hands-on GATK tutorials in this workshop will be conducted on Terra (http://terra.bio), a new platform developed at Broad in collaboration with Verily Life Sciences for accessing data, running analysis tools and collaborating securely and seamlessly. (If you’ve heard of or been a user of FireCloud, think of Terra as the new and improved user interface for FireCloud that makes doing research easier than before!)

All accepted registrants will attend the first day of the workshop. You may select subsequent days à la carte.

Day 1: Thursday, March 21, 2019 — Introductory topics and hands-on tutorials (Required).
We'll start off with introductory lectures on sequencing data, preprocessing, variant discovery, and pipelining. Then you'll get hands-on with a recreation of a real variant discovery analysis in Terra.

Day 2: Friday, March 22, 2019 — Germline short variant discovery (Optional).
Through a combination of lectures and hands-on tutorials, you'll learn: germline single nucleotide variants and indels, joint calling, variant filtering, genotype refinement, and callset evaluation.

Day 3: Tuesday, March 26, 2019 — Somatic variant discovery (Optional).
In a format similar to Day 2, you'll learn: somatic single nucleotide variants and indels, Mutect2, and somatic copy number alterations.

Day 4: Wednesday, March 27, 2019 — Pipelining and additional skills for working in Terra (Optional).
You'll learn how to write your own pipelining scripts in the Workflow Description Language (WDL) and execute them with the Cromwell workflow management system. We will also cover additional skills to help you do an end-to-end analysis in Terra.

This hands-on Hail 0.2 tutorial will be led by members of the Hail team, based in the Neale lab in the Stanley Center.  

Hail is an open-source, general-purpose, Python-based data analysis tool with additional data types and methods for working with genomic data. Similar to the R or Python scientific computing stacks, Hail supports data frame queries, statistics, linear algebra, and plotting, both interactively and with scripts. Unlike these stacks, Hail:

- scales from laptop to large compute cluster or cloud, with the same code
- is designed to work with datasets that do not fit in memory
- has first-class support for multi-dimensional structured data, like genomic data

At Broad, Hail is the analytical engine behinds dozens of studies, the Genome Aggregation Database (gnomad.broadinstitute.org), and the Neale lab mega-GWAS (nealelab.is/uk-biobank). Beyond Broad, Hail is used by academia and industry on data ranging from mouse models to GTEx.

Target audience: Scientists analyzing genomic variant datasets and their relationship to phenotypes, gene expression, or other data. Participants may pre-install Hail or access it via the cloud in their browser.