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VIZBI 2013 Workshop on Visualizing Biological Data schedule

Tuesday 19th March 2013

  • Animation with Maya

    by Drew Berry

    This tutorial will describe two techniques for creating natural-looking cellular and molecular assets in Maya in vast quantities with appropriate dynamics and behaviours, that can be rendered in seconds.

    The first technique is the workflow for Sprite particles which are ideal for populating a scene with thousands of brownian-movement molecules that can output rendered frames in less than a second. The Sprite technique has been around since the 1970's and the method I will present should be broadly applicable to any of the major animation packages.

    The second technique is PaintEffects, an Autodesk (http://usa.autodesk.com/) proprietary system that originated in Maya in 2000. I will demonstrate the workflow for using PaintEffects to 'grow' 3D blood vessels and other cellular tissues.

    Participants will need their own laptop with any version of Maya (http://usa.autodesk.com/maya/) installed.

    At 9:30am to 1:00pm, Tuesday 19th March

    In Broad Institute

  • Blender

    by Engel Sanchez

    Blender 3D (http://blender.org/) is a full featured 3D creation suite. It has everything you need to create, animate and render 3D masterpieces.

    In this tutorial, we'll take a tour of some of Blender's most popular features. We'll start with fundamentals such as Box modeling, sculpting and materials, and move on to basic animation, rigging, skeletal animation and basic programming to extend Blender.

    Prerequisites: You will need to download the Blender program from the Download Page (http://blender.org/download) and make sure it runs on your system before the day of the workshop. A 3 button mouse is also strongly recommended, and a numeric keypad will also help.

    See the VIZBI 2013 Blender tutorial page (http://engelsanchez.net/vizbi2013/) for full information and useful links.

    At 9:30am to 1:00pm, Tuesday 19th March

    In Broad Institute

  • IGV - Integrative Genomics Viewer

    by Jim Robinson and Helga Thorvaldsdottir

    In this tutorial participants will learn to view and explore data in the Integrative Genomics Viewer (IGV).
    IGV is a widely-used desktop application for interactive visual exploration of a wide range of genomic data types, including sequence alignments, genomic annotations, copy-number, gene expression, and clinical data. Participants will learn: (1) the basics of using the IGV application, (2) options for visualization of next-generation sequence (NGS) alignment data and array-based data, (3) how to integrate clinical data, and (4) how IGV supports visual inspection of NGS data, including variant call validation, interpretation of insert sizes and pair orientation in paired-end sequencing data, and inspection of genomic rearrangements.

    The tutorial includes both lectures and hands-on exercises, so bring a laptop.

    At 9:30am to 1:00pm, Tuesday 19th March

    In Broad Institute

  • Illustrator

    by Andrew Tang

    Need to create publication quality figures? Adobe Illustrator is the tool of choice. In this tutorial you’ll learn what makes Illustrator such a powerful tool. I will cover the basics of this jack-of-all-trades graphics software from manipulating your data to creating figures from scratch and how to incorporate this into your workflow.

    At 9:30am to 1:00pm, Tuesday 19th March

    In Broad Institute

  • Introduction to D3

    by Christian Stolte

    Data visualization on the web has come a long way in the past few years,
    and JavaScript plays a major role in this context.<br>&nbsp;<br>
    D3 (= Data-Driven Documents) is a JavaScript library for presenting data as
    dynamic visualizations of large datasets, rendered as SVG in the browser,
    complete with animation and interaction. You will learn how to bind data
    to elements, apply transforms to generate and modify content, and how to
    create interactive visualizations for the web. We'll cover how the basic
    elements of web development, such as the document object model (DOM), CSS,
    and Javascript, work together to create standards-based data graphics. You
    will learn how to get started creating dynamic visualizations with D3 by
    working through real-life examples.<br>&nbsp;<br>For this workshop you should have basic knowledge of JavaScript, HTML, and
    CSS. Bring your laptop with a text editor of your choice.

    At 9:30am to 12:30pm, Tuesday 19th March

    In Broad Institute

  • Tableau

    by Zach Leber

    Tableau (http://www.tableausoftware.com/) is general purpose data visualization software that's been used at the Broad Institute since 2010 for analyzing, monitoring, and optimizing genomic sequencing operations. The Broad's cancer group is also using Tableau for genotype expression data. Tableau connects to all standard business databases (e.g. Oracle, MySQL) and file types (e.g. CSV, Excel).

    Pre-configured Windows laptops with Tableau installed will be provided for students. Broad sample data will be used for most of the examples, but students should bring their own data in a spreadsheet or text file on a flash drive. Data files should be formatted according to the guidance provided in this tableau knowledgebase article (http://kb.tableausoftware.com/ar...).

    At 9:30am to 1:00pm, Tuesday 19th March

    In Broad Institute

  • UCSF Chimera

    by Scooter Morris

    UCSF Chimera is a platform for the visualization and analysis of the structures of biological molecules at multiple scales and resolutions.

    This introductory tutorial will focus on the visualization of molecular structures in general and how to achieve those visualizations in Chimera. The course will provide a mixture of lecture and hands-on exercises that will introduce participants to Chimera's commands and tools, and how to use those commands and tools to visualize proteins, nucleic acids, volumes, and large complexes.

    The latest release of Chimera (1.7) includes a new facility for creating simple molecular animations. We spend some time at the end of the tutorial exploring this new tool and how to utilize it for creating storyboards for more sophisticated animation packages.

    Participants should bring their own laptop. The latest release of Chimera will be provided at the start of the tutorial. Participants are also encouraged to bring their own datasets or molecules of interest. No previous experience with animation packages or molecular visualization tools is required.

    At 9:30am to 1:00pm, Tuesday 19th March

    In Broad Institute

  • GenomeSpace

    by Michael Reich

    GenomeSpace (http://www.genomespace.org/) is an environment that brings together a diverse set of computational tools, enabling nonprogramming scientists to easily combine the tools’ capabilities through a user-friendly point-and-click interface. It offers a common space to create, manipulate and share an ever-growing range of genomic visualizations and analyses. GenomeSpace features support for cloud-based data storage and analysis, multi-tool analyses, automatic conversion of data formats, and ease of connecting new tools to the environment.

    A set of six “GenomeSpace-enabled” seed tools developed by collaborating organizations provides a comprehensive platform for the analysis of genome data: Cytoscape, Galaxy, GenePattern, Genomica, Integrative Genomics Viewer, and the UCSC Genome Browser. The extensible format of the system has empowered a wider range of analyses through the continual addition of new tools and resources.

    Participants will learn how to use GenomeSpace to utilize the visualization and analysis capabilities of multiple tools in several research scenarios. Through the demonstration of a number of short analysis “recipes” we will give participants the essential elements to construct powerful integrative genetic and genomic analyses.

    At 2:30pm to 6:00pm, Tuesday 19th March

    In Broad Institute

  • Introduction to uPy, ePMV & autoPACK

    by Graham Johnson

    "This workshop will overview and teach four related software projects via a collection of hands-on tutorials.<br/>
    <br/>Participants will:
    <br/>1. Create a collection of professional quality scientific visualizations
    <br/>2. Learn how to use, write, and modify scripts and GUI development code that will automatically function inside of a growing number of 3D animation software hosts that currently include: Autodesk’s Maya and 3D Studio Max, Maxon’s Cinema 4D, Blender, and the molecular graphics viewer DejaVu.
    <br/><br/>Two of the projects covered, <a href=""http://upy.scripps.edu"">uPy</a> and <a href=""http://www.autopack.org/"">autoPACK</a>, have broad scientific and artistic applications. We will also explore two highly developed plugins written in uPy: <a href=""http://epmv.scripps.edu/"">ePMV</a> and <a href=""http://www.cellpack.org/cellpackchallenge2012"">cellPACK</a>, to learn these tools of molecular modeling and animation while exploring the potential of the uPy programming API from a user’s perspective.<br/>
    <br/>
    <em>Prerequisites</em><br/>Participants <u>must</u> bring their own laptop with at least one of the following uPy compatible host environments preloaded: Maya, Cinema4D, or Blender.<br/>We encourage students experienced with 3D animation software to use their favorite package (note - 3DS Max can be used, but its uPy support is limited).<br/>
    We recommend that beginners and intermediate-level 3D users install Cinema 4D so that they can follow the tutorials efficiently through its user-friendly interface. If you do not already have this, then please fill out the <a href=""http://www.maxon.net/products/demo-version/download-form.html"">Cinema4d demo registration</a> page in order to download a trial version.<br/><br/>For full details of the workshop program see <a href=""http://www.mesoscope.org/workshops/vizbi-2013-upy-epmv-autopack-workshop"">the uPy ePMV and Autopack workshop site</a>

    At 2:30pm to 6:00pm, Tuesday 19th March

    In Broad Institute

  • Processing

    by Mark Shifferli

    Processing (http://processing.org/) is an open-source programming environment tailored to generating images and animations. It features a straightforward programming language that is easy to learn, and with it you can build rich interactive visualizations for complex datasets. When it comes time to share your work, Processing allows you to save images or .pdf's, or you can put it in a web page using Processing.js (http://processingjs.org/). For more intense jobs, Processing also provides a fully compatible java library.

    In this tutorial, we will start with the basics of making a Processing sketch and progress to loading data and building interactive visualizations. Processing is particularly well suited to quickly sketching ideas, so we will spend some time exploring different presentations. We will also learn to save your work for print or the web.

    Participants will need to bring their own laptops, and install Processing, which can be downloaded at http://processing.org/download/ . Extra credit for those who download Processing.js (http://processingjs.org/download/) too.

    At 2:30pm to 6:00pm, Tuesday 19th March

    In Broad Institute

  • StratomeX & enRoute: Integrative Visualization with Caleydo

    by Nils Gehlenborg and Alexander Lex

    One of the premier challenges of visualization in biology is the integration across many molecular data types to provide a comprehensive view of complex phenomena. In this tutorial we will introduce the Caleydo framework and focus on two tools that we have developed to address this challenge. The goal of the workshop is two-fold: first, we will introduce participants to these integrative visualization techniques from a visualization research perspective. Second, we will teach how these visualization tools can be applied to large-scale genomics data sets to explore pathways and to identify and characterize disease subtypes across hundreds of samples, respectively.

    Caleydo Website: http://www.caleydo.org
    StratomeX for The Cancer Genome Atlas: http://compbio.med.harvard.edu/t...

    At 2:30pm to 6:00pm, Tuesday 19th March

  • User experience design: empathy, insight and evaluation

    by Francis Rowland

    This practical, hands-on workshop introduces user experience (UX) design concepts and practices. We will cover how to gain insights by empathising with your audience, how to frame your data in the most effective ways, and how to evaluate visualisation systems.

    You know your data inside and out. You know the science. You know the software and the tools. But how do you get to know your audience: the consumers of your data visualisations? In this workshop, Francis Rowland will introduce some of the concepts and practices that he applies in his work as a UX designer at the EMBL-European Bioinformatics Institute.

    It can be challenging to close the gap between what your audience wants to know and what stories your data has to tell. As interactive visualisation becomes more and more relevant in the working world of science, the challenges only multiply - and that's where things start to get really fun. Bring your pens, paper and an open mind (laptops are welcome but not strictly necessary) and let's get started.

    At 2:30pm to 6:00pm, Tuesday 19th March

    In Broad Institute

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