Past Workshops

2013
Visual Representation for Exploring and Explaining Scientific Data Visual representation can serve two distinct purposes: to guide the data-exploration process as the scientific story is still unfolding and to communicate research findings. Each goal entails a different approach to data representation, but sound graphic design principles are important in both. This workshop will focus on data-visualization techniques to parallel the research trajectory from lab to publication. Prospective attendees will be guided through essential design principles, graphical methods for depicting information, and software tools for implementing visualization ideas. Hands-on activities will give participants opportunities to put concepts into practice.	May 10

Intro to RNA-Seq RNA-Seq is revolutionizing our ability to analyze the transcriptome. This seminar will present participants with an overview of RNA-Seq principles, experimental considerations, steps of the RNA-Seq analysis process, and current state of the art. It will provide the basis for future in-depth RNA-Seq courses and workshops.	May 7	Workshop Materials

GenePattern In a half-day, hands-on format, participants learn to use GenePattern features, including an intuitive graphical user interface for users at all levels of computational sophistication, a comprehensive repository of over 180 tools for the analysis of gene expression, sequence variation, proteomics, and more, and a pipeline environment that allows users to chain tasks together to create and share reproducible analysis workflows.	May 3

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.	April 12	Workshop Materials

Functional Genomic Screens in the RNAi Platform The RNAi Platform workshop 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 use these resources as well as computationalists who want to understand more about the the biological mechanisms and and experimental approaches underlying the data sets that emerge. We will cover the range of perturbations available in the Platform, including shRNAs, ORFs, and TALENs, 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.	April 5	Workshop Materials and Videos

Genome Assembly This half-day workshop is intended as an introduction to the concepts of assembly and assembly analysis. The content is well-suited to non-experts who wish to learn about the fundamentals of assembly algorithms and basic best practices for understanding levels of quality in an assembly. Basic understanding of the concepts of genome sequencing and genome assembly is expected. The first third of this course will focus on what an assembly is, and how changes in sequencing technology have impacted assembly algorithms. We will provide insights into how assemblers work, and why assembly is still an open problem. Attendees are expected to gain a basic understanding of current assembly algorithms. This section contains an interactive problem-solving session designed to develop understanding of assembly algorithms. The second two-thirds of the course will focus on utilizing and analyzing genomic assemblies. We will outline why assemblies are not perfect, and explain how not all assemblies are created equal. Participants should leave with a good understanding of what metrics should be assessed when judging the quality of an assembly. This session contains an interactive analysis session where participants will be able to look at real assemblies to diagnose issues.	March 20	Workshop Materials

RNA-Seq Basics This workshop will cover the basic conceptual ideas behind library construction, sequencing, and initial analysis of RNA-Seq data. The workshop is aimed at biologists who want to learn the basics of RNA-Seq analysis, computationalists who want to understand more about the basics of RNA-Seq data generation, or anyone who is interested in RNA-Seq but is not familiar with basic high throughput sequencing technologies. We will start with very basic concepts from three perspectives: generating high throughput (e.g., Illumina) sequencing data; making RNA-Seq libraries; and understanding mRNA structure, annotation, and quantitation. We will proceed through the steps of basic sequencing into the common first pass methods for analysis. Prospective attendees who are already familiar with the majority of these concepts and are looking for a more in depth or hands-on workshop on specific RNA-Seq techniques are advised to look for our more advanced workshop in May.	March 6	Workshop Materials

Differential Expression analysis of RNA-Seq with the Tuxedo Tools RNA-Seq is now a routine assay for measuring gene expression, but the analysis of the data can be daunting. This course will cover basic principles of RNA-Seq analysis and include hands-training for the "Tuxedo Tools". Users will learn to run TopHat, Cuffdiff, and CummeRbund to detect differentially expressed genes and transcripts. Objective Participants in this workshop will learn fundamental concepts of RNA-Seq analysis and be able to perform a basic differential analysis at gene- and isoform-resolution using the Tuxedo Tools. Skill Level Those new to RNA-Seq. Familiarity with UNIX and/or R is a strong plus. Prerequisites Users are strongly encouraged to familiarize themselves with R prior to coming to the workshop. You will get much more out of this workshop if you are comfortable with starting and stopping an R session and performing very simple tasks such as opening and viewing files in R. Users are also encouraged to have a look at ggplot2, which is a beautiful plotting package written in R. CummeRbund, which we will use to explore our RNA-Seq data, is built on top of ggplot2. There is an excellent, easy to read book on ggplot2, and you can find sample chapters here: http://ggplot2.org/book/. Chapter 2 is available for free, and you are strongly encouraged to try running the bits of R code in chapter 2 on your own to get a feel for what exploring data with R and ggplot2 is like. The entire book is available through Amazon.com and is an extremely worthwhile read.	January 11

2012
Proteomics: Everything you always wanted to know but were afraid to ask This 2-half day course will present all 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. The first half day will cover the essentials of the technology; the most important classes of proteomics experiments and the specific sample requirements for each; the software for proteomic data analysis and its proper use; quantitative MS approaches applicable to global proteome and PTM analyses, including metabolic labeling methods, chemical labeling approaches and label-free methods; and the basics of targeted, hypothesis-driven MS using multiple reaction monitoring MS. The second half-day session will use case studies to focus on the data produced by each of the key classes of proteomics experiments described on day one (i.e., global proteomics, global PTM analysis; affinity proteomics and targeted, hypothesis-driven proteomics). Data analysis approaches and statistical methods key to confident assignment of true differential proteins/peptides will be presented. We will finish with a primer on useful tools for annotating the MS results and to extract knowledge and organize results into pathways.	December 10 Technology, samples and experiments December 11 From Lists to biological knowledge	Workshop Materials and Videos

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. 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.	December 4, 5	Workshop Materials and Videos
The workshop will last two days, divided into lecture-style sessions in the morning and optional hands-on sessions in the afternoon (note that for practical reasons, attendance at the latter will be limited, so be sure to sign up early). In the morning, you’ll hear from the GATK development team and invited guests, who will explain the rationale, theory and real-life applications of the Best Practices. In the afternoon, the GATK team will help you work through interactive exercises and tutorials in which you will apply the Best Practices to real datasets. All participants should be familiar with general next-gen sequencing terms and data formats. The lecture-based morning sessions are open to all existing, new or prospective users of the GATK. The hands-on afternoon sessions are restricted to existing users of the GATK who are familiar with the command-line work environment and at least capable of running simple analyses as described in an online tutorial.

RNA-Seq Basics This workshop will cover the basic conceptual ideas behind library construction, sequencing, and initial analysis of RNA-Seq data. The workshop is aimed at biologists who want to learn the basics of RNA-Seq analysis, computationalists who want to understand more about the basics of RNA-Seq data generation, or anyone who is interested in RNA-Seq but is not familiar with basic high throughput sequencing technologies. We will start with very basic concepts from three perspectives: generating high throughput (e.g., Illumina) sequencing data,;making RNA-Seq libraries; and understanding mRNA structure, annotation, and quantitation. We will proceed through the steps of basic sequencing into the common first pass methods for analysis. Prospective attendees who are already familiar with the majority of these concepts and are looking for a more in depth or hands-on workshop on specific RNA-Seq techniques are advised to look for our more advanced workshops in spring 2013.	November 27	Workshop materials

Metabolomics: Experimental design, methods, and analysis Metabolomics is the systematic analysis of endogenous metabolites in a biological sample and can be applied toward deciphering both normal physiology and disease pathogenesis. This initial workshop will present an overview of liquid chromatography tandem mass spectrometry (LC-MS)-based metabolomics methods. We will discuss practical considerations for design of experiments using cellular and animal models as well as clinical studies. We will also discuss state-of-the-art analytical tools and approaches to data analysis.	November 7

A picture is worth a million numbers: Extracting quantitative information from biological images using CellProfiler 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. This workshop is open to all experience levels. Novices to biological image analysis are encouraged. Basic knowledge of fluorescence microscopy and digital image acquisition is helpful.	November 2

Introduction to NGS Visualization with IGV In this course participants will learn to view next generation sequence (NGS) alignment data in the Integrative Genomics Viewer (IGV). Topics covered include single nucleotide variants, insertions and deletions, genomic rearrangements, and transcription abundance. The course will include both lecture and hands-on exercises.	October 5

RNA-Seq RNA-Seq is revolutionizing our ability to analyze the transcriptome. This seminar will present participants with an overview of RNA-Seq principles, experimental considerations, steps of the RNA-Seq analysis process, and current state of the art. It will provide the basis for future in-depth RNA-Seq courses and workshops.	June 25	Workshop materials

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.	May 25

GenePattern In a half-day, hands-on format, participants learn to use GenePattern features, including an intuitive graphical user interface for users at all levels of computational sophistication, a comprehensive repository of over 180 tools for the analysis of gene expression, sequence variation, proteomics, and more, and a pipeline environment that allows users to chain tasks together to create and share reproducible analysis workflows.	May 21