2012 Workshops

       
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