VISUALIZING BIOLOGICAL DATA VIZBI

Blender is a complete package for 3D content creation (from modelling to animation, rendering and game elaboration) developed as an open source project, which is increasingly popular for academic work. Using this tool, it is possible to visualize in an animated way any 3D subject, from atomic scale molecules to entire organisms. The workshop will introduce Blender and the Virtual Worm project. The Virtual Worm project is an attempt to construct an anatomically accurate 3D model of the nematode Caenorhabditis elegans, for the purpose of education, data visualization, and integration into the C. elegans database WormBase.org. This tutorial will focus on basic Blender operation and interface, and cellular/organism anatomy applications using the Virtual Worm as an example.

Animation can effectively communicate multistep biological processes. This tutorial will provide an introduction to molecular visualization and analysis tools and to molecular animation techniques. During the first half of the tutorial, we will cover the basic capabilities of molecular visualization tools, including the types of structures and data sources used for molecular visualization. Participants will learn how to load, visualize, and manipulate 3D structures with relevant representation styles and how to save images and animations for publication.

During the second half of the tutorial, we will focus on molecular animations, highlighting current and future capabilities in Chimera that support both simple and complex animations. In particular, we will demonstrate how to use Chimera "scenes" to quickly and easily storyboard events; discuss how to use Chimera's built-in command language to generate simple animations and save them using Chimera's movie recording tools. Lastly, we will quickly demonstrate other tools currently available to produce more involved animations like mMaya and ePMV.

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics and funded by the US National Institutes of Health (grants 2P41RR001081-35 and 9P41GM103311-35).

We will demonstrate and explore a variety of Cytoscape plugins for analysis and visualization. In particular, we will use the clusterMaker plugin to cluster networks and attributes; the Network Analysis plugin to explore the properties of networks; the BiNGO plugin to calculate overexpression of GO categories; and the structureViz and chemViz plugins to add structural visualization and information to the network.

Processing is an open-source programming environment with a vivid community. It lets you quickly sketch programs and try out visualization ideas of your own. Unlike other tools, such as Blender, it has an extremely flat learning curve. In the beginning you can use it as a sand box for creating interactive 2D and 3D animations, but it allows you to quickly step out of the box and harness the power of its environment.

For Processing 1.0 this environment used to be Java with a quickly growing numberof libraries. Then - with the advent of HTML 5, Processing.js became a popular alternative, making use of the HTML Canvas and WebGL.

This tutorial will take you all the way from creating Processing.js-sketches with Processing 2.0, to extending their capabilities via javascript. You will make your visualizations import data via the web and integrate GUI elements from your favorite javascript framework. Finally you will learn how to use external libraries such as toxiclibs.js, and apply shader hacks for 3D visualization.

This tutorial will introduce several RNA Visualization and computational approaches that allow the prediction of RNA structure from sequence. We will briefly overview the main sources of RNA data, and introduce the main data formats used to encode structural information. Tutees will have the opportunity to gain practical experience in using RNA structure prediction software and visually evaluate their output against known RNA 3D structure.
Tools that will be covered:
- Structure prediction: RNAFold, RNAalifold, LocARNA.
- Visualization and assessment: VARNA, Pseudoviewer, VIENNA web server, Jalview
- 3D Structure annotation: RNAView, Jmol

Prerequisite software: Java + some Web browser

We will present fundamental principles of graphic design and visual communication that will help you create more effective interactive and print visualizations. You will learn how the purposeful use of salience, color, consistency and layout can help communicate large data sets and complex ideas with greater immediacy and clarity. We will illustrate how these principles were implemented in ABySS-Explorer to visualize genome assemblies, an example to show you ways to apply design ideas to your own project. At the end of the tutorial, you will apply what you have learned in an interactive group session in which you will design a figure illustrating a biological process. Complete course notes and presentations from this tutorial are available at http://mkweb.bcgsc.ca/vizbi/2012/

Lunch Break (13:00 - 14:30)

3D image datasets such as MRI can be visualised and segmented using the PC-based software tool, Amira (Visage Imaging GmbH, 12163 Berlin, Germany). This allows anatomical models to be produced, combined and compared. It facilitates quantitative analysis such as volumetric studies and texture analysis.
 
(i) Visualisation: amira can view 2D images from any orientation within the 3D data set.
(ii) Segmentation: 3D surface representations can be produced by surface rendering the 3D finite element meshes generated from segmenting a region of interest. A variety of segmentation tools are available in amira.
(iii) Image Processing: A number of additional editors are present that allow various data manipulation, for example to crop, resample or transform the datasets.
 
This tutorial plans to summarise the main features of amira. In it, I will explain how to (i) load and view data, (ii) segment data, (iii) save and export data, (iv) use the various editors available. We will also discuss practical tips when segmenting data and protocols of producing anatomical models.

Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The phylogenetic software package ARB (latin, 'arbor' = tree) has been developed for nearly 20 years to cope with this deluge of data. It has primarily been implemented to handle ribosomal RNA data, but can be easily used for any kind of sequence data. Besides import/export, data management and alignment functions a powerful sequence editor is implemented which can be used for nucleic acid as well as amino acid sequences. Furthermore, a unique maximum parsimony approach allows the reconstruction and evaluation of large trees which is a prerequisite for accurate phylogenetic classification. To facilitate in-depth analysis of molecular data, a comprehensive selection of software tools is integrated into ARB.

The interactive software tool ARB was recently supplemented by SILVA (latin, 'silva' = forest) to provide a central, comprehensive web resource for up to date, quality controlled databases of aligned small (18S/18S)- and large (23S/28S) subunit rRNA sequences from the Bacteria, Archaea and Eukarya domains.

During the tutorial we will cover how to browse SILVA for sequences of interest and how to import/export sequences to ARB. Afterwards, a general workflow of alignment, tree reconstruction and probe design will be presented using ARB.

During this tutorial, we will demonstrate how to develop plugins and apps for Cytoscape. Cytoscape is undergoing a significant rewrite for Cytoscape 3.0. As part of this rewrite plugins and plugin development will change in a number of ways. This tutorial is targeted as individuals who want to take advantage of the network visualization and analysis capabilities of Cytoscape and extend it by adding new visual or analytical capabilities. This will focus primarily on the existing version of Cytoscape, but we will also highlight how things will change in Cytoscape 3.0 when Cytoscape plugins become Cytoscape "apps". We will focus on the Cytoscape API and how to quickly and easily extend Cytoscape's capability with your own algorithms. We will also discuss how to make your plugin available via the Cytoscape PluginManager and how to take advantage of the capabilities of other plugins through the CyCommand API. Attendees to this tutorial should be familiar with Java and Cytoscape.

Recent improvements in JavaScript performance, along with widespread support for SVG, are changing the landscape for data visualization on the web. Rich dynamic visualizations of large datasets, complete with animation and interaction, can now be built directly in the browser. Data-Driven Documents (D3) is a new JavaScript library for visualizing data using web standards. D3 lets you harness the full capabilities of your browser, including useful developer tools such as the element inspector. Similar to jQuery, D3 allows you to bind data to elements and apply transforms to generate and modify content. This enables an expressive range of visualizations to be constructed quickly. In this workshop, you will create interactive visualizations for the web. We'll cover the basics of web development, such as the document object model (DOM), and how to apply these standards to data graphics. You will learn how to compose dynamic visualizations with D3 by working through both playful and powerful examples.

The Integrative Genomics Viewer (IGV) is a 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. A particular strength of IGV is its ability to visualize very large datasets, for example, deep coverage sequence data from whole-genome scans or high-resolution copy number data from thousands of samples. In this tutorial we will cover integration of genomic and clinical data, visualization and interpretation of NGS sequence alignments, and preparation of files, including the use of igvtools and other utilities.

This workshop will introduce participants to the power and flexibility of the 3D software package Maya a workhorse in the film industrys special effects and animated feature films. This hands-on workshop will cover all the major phases of the 3D production pipeline: modeling, surfacing, animation, dynamics and rendering. We'll focus on how Mayas broad set of tools can be adapted for biovisualization and, specifically, how the free and open source Molecular Maya (mMaya) toolkit allows for importing and animation of structural datasets within Maya. By the end of this workshop, participants will 1) have a strong sense of Maya's capabilities and its potential relevance to their own research, 2) have created a molecular binding animation, and 3) be introduced to a wealth of free learning materials for continued training.

It is recommended that participants bring their laptops with Maya installed. Autodesk now offers a free 36-month full-featured trial version of Maya for academics (students and/or faculty):

http://students.autodesk.com/

Participants are also welcome to install Molecular Maya before the workshop:

http://www.molecularmovies.com/toolkit/

(but the latter is not required - it will just take a minute to install this free plugin during the workshop).

Visualizing Single Genome Data
Session Chair: James Procter

Visualizing Transcript Data
Session Chair: John Quackenbush

Visualizing Proteins & Complexes
Session Chair: Gaël McGill

Visualizing Cellular Systems
Session Chair: Nils Gehlenborg

Visualizing Organism Data
Session Chair: Richard Baldock

Alignments & Phylogenetics
Session Chair: Chris Creevey