2014 Workshops
Public Small-Molecule Databases: Chembank, Pubchem, BARD, and Beyond Several bioassay data-storage and data-analysis systems exist that provide public access to chemical biology, computational chemistry, and bioinformatics resources. The development of these resources has undergone multiple generations of refinement in terms of data structure, data sources, and analytic capabilities. This course will briefly cover the evolution of these resources, highlighting aspects of each, then will focus on use cases for the more modern systems. This will include a focus on one of the most recent systems, the BioAssay Research Database (BARD), developed in part by a team from the Broad. Interactive demonstrations on data capture and data mining will be included. Participants are encouraged to bring information on a sample bioactive small molecule of interest to their research to be used in the interactive portion of the class. If time allows and depending on participant interest, methods for acquiring physical samples of small molecules may also be covered. |
December 17 | |||
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. |
December 8 |
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Connectivity Map 101 The Connectivity Map (CMap) is composed of ~1.4 million gene expression profiles. In order to effectively mine this database, the CMap team has developed a suite of WebApps and command-line tools. This workshop will provide an introduction to CMap and training on the most up-to-date CMap apps and tools. |
November 24 |
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Drug Discovery 101 As the cost of generating new therapies has risen due in part to clinical failures, an understanding of past efforts and future directions may help spur changes within the pharmaceutical industry. This course will address:
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November 3 | Workshop Videos | ||
Firehose Workshop This workshop will have 4 sections.
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October 2 | |||
Statistical Genetics This workshop provides an introduction to the basic principles of statistical genetic analysis. This course is targeted for individuals who are interested in learning the basics of genetic analysis. Specific areas of focus for the course include: study design considerations for genetic association tests, quality control (QC) procedures for genetic data, basic analysis of genome-wide association SNP data, and introduction to rare variant testing approaches. The workshop will be a blend of lectures introducing each of these topics and then hands-on practical application, in particular for QC and common variant analysis. Tutorial datasets will be provided for the introduction to the analysis of genetic data. Participants will not need to bring a laptop, as computers will be provided. At the end of the workshop, participants should have a basic understanding of the elements of genetic analysis for common and rare variation. In particular, this workshop will provide a foundation for starting genetic analysis of real data and an introduction for how best to learn more about current techniques. The practical components of the workshop will include command line work, so basic familiarity with Unix environment is strongly recommended. |
September 29 | |||
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. |
September 19 |
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GenePattern Participants will learn to use GenePattern features, including an intuitive graphical user interface for users at all levels of computational sophistication; a comprehensive repository of clustering, prediction, preprocessing, and visualization modules for analysis of microarray data; a pipeline environment that allows users to chain tasks together to create and share methodologies; a module integration environment that allows rapid, code-free integration of new tools; and a programming environment that allows users to access GenePattern modules from the Java, MATLAB, and R programming languages. |
September 12 | Workshop Materials | ||
Strategies for Visualizing Data Data visualization is becoming increasingly important in biomedical research as a means to explore data for patterns and relationships. Such exploration, driven by the graphical representation of information, is the critical first step to inform subsequent computational and machine-driven approaches to data analysis. The process requires us to further define clear objectives and improved implementation to be successful. Data for the most part have no natural form or “look” — we have to make choices about how they are displayed. Each decision can bring out certain kinds of patterns in data while hiding others. We rely heavily on our intuition, common sense, and precedent in published material when we visually depict data. This is largely an unscientific process. In this workshop we will explore systematic approaches that rely on core graphic design principles and vision science (i.e., how we decode information encoded in graphical form) to develop effective visualizations of data. |
July 21 | Workshop Materials | ||
Introduction to the Integrative Genomics Viewer (IGV) In this course, participants will learn to use the Integrative Genomics Viewer (IGV) to view different types of genomic data. Topics covered include:
The course will include both lecture and hands-on exercises. |
June 27 | 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. |
June 6 | |||
Single-Cell Genomics: Theory & Practice Emerging genomic technologies now allow for deep and unbiased profiling of single cells and represent powerful approaches for characterizing and dissecting cellular behaviors in complex and heterogeneous tissues. This workshop is intended to provide a practical and hands-on introduction to the experimental and computational aspects of single-cell analysis, with an emphasis on single cell RNA-Seq. The workshop will be divided into two portions: first, we will describe and demonstrate experimental approaches to single cell genomics; then, we will introduce computational approaches for QC and analysis of single cell data, focusing on recently published single-cell RNA-Seq datasets. |
June 2 |
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Genome Engineering Using CRISPR-Cas9 Recent advances in genome-engineering technologies based on the CRISPR-associated RNA-guided endonuclease Cas9 are enabling the systematic reverse engineering of mammalian genome function. Derived from prokaryotic immune systems, Cas9 can be targeted to specific locations within the complex, mammalian genome using short RNA guides. DNA sequences within the endogenous genome and their functional outputs are now easily edited or modulated in virtually any organism of choice, empowering researchers to elucidate the functional organization of the genome at the systems level, as well as establish causal linkages between genetic variations and biological phenotypes. In this workshop, we describe the applications of Cas9 for a variety of research or translational applications and highlight challenges and important experimental considerations. The development of these remarkable microbial defense systems is driving innovative applications from basic biology, to biotechnology and medicine. |
May 13 | |||
Charting the Epigenome with ChIP — Basic Analyses of ChIP-Seq Data ChIP (chromatin immunoprecipitation) is a very powerful technique that enables the localization of proteins on DNA throughout the genome. The technique relies on the selective enrichment of a chromatin fraction containing a specific antigen, by immunoprecipitation. Antibodies that recognize a protein or protein modification are used to capture the chromatin (protein-DNA complex), and in the contemporary method of ChIP-Seq, next-gen sequencing libraries are derived from the recovered DNA. The libraries are sequenced and the recovered sequences are aligned to a genomic scaffold to map the locations of the antigen recognized by the antibody. The ChIP technique can be used in any area of research to further elucidate gene function and regulation in their native state. Application of ChIP to the genome wide localization of DNA binding proteins, transcription factors, chromatin modifying enzymes, and histone modifications has helped develop an understanding of the mechanisms for the regulation of chromatin organization. These methods have contributed to our understanding of embryogenesis and tissue specific cellular differentiation, while aberrant chromatin structure is associated with development disorders and other diseases, such as cancer. The workshop will cover the following topics:
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May 9 | Workshop Materials and Videos | ||
Statistical Genetics This workshop provides an introduction to the basic principles of statistical genetic analysis. This course is targeted for individuals who are interested in learning the basics of genetic analysis. Specific areas of focus for the course include: study design considerations for genetic association tests, quality control (QC) procedures for genetic data, basic analysis of genome-wide association SNP data, and introduction to rare variant testing approaches. The workshop will be a blend of lectures introducing each of these topics and then hands-on practical application, in particular for QC and common variant analysis. Tutorial datasets will be provided for the introduction to the analysis of genetic data. Participants will not need to bring a laptop, as computers will be provided. At the end of the workshop, participants should have a basic understanding of the elements of genetic analysis for common and rare variation. In particular, this workshop will provide a foundation for starting genetic analysis of real data and an introduction for how best to learn more about current techniques. The practical components of the workshop will include command line work, so basic familiarity with Unix environment is strongly recommended. |
April 14 |
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Genetic Perturbations for Functional Genomics: RNAi, CRISPRs, ORFs The Genetic Perturbation Platform (formerly known as RNAi 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 13 |