VIZBI 2011

David Shattuck (http://www.bit.ly/qWdhpD) presents a survey of the rapidly evolving field of biomedical imaging, and includes some stunning images from his own work on brain imaging. He also discusses the role played by data visualization, which is critical in diagnosis, validation, and interpretation. He identifies the key challenges as keeping apace with increasing data complexity, size, and interconnectedness. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO.

Bang Wong (http://www.bangwong.com) welcomes delegates to VIZBI 2011. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO.

Manuel Lima (http://www.visualcomplexity.com) outlines historical factors behind the current outburst of visualization, then gives an eclectic survey of recent projects that visualize complex data in a clear and compelling manner, especially networks. He also highlights general strategies for managing visual complexity. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO.

Robert Kuhn (http://www.bit.ly/UCSCgb) discusses visualization and navigation of data mapped onto a reference genome coordinate system. He shows how the widely-used UCSC genome browser enables comparisons between multiple organisms and handles next-generation sequence data. He also outlines plans for managing data on personal genomic and on chromatin 3D folding. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO.

Bradley Bernstein (bernsteinlab.org) explains how upcoming advances in epigenomics data on chromatin and genome reorganizations promise to give insights as revolutionary and fundamental as genomic sequences. He also highlights the inadequacies of current visualization methods, particularly for showing data on regulatory elements, cell-types, cell lineage, SNPs, and GWAS. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (vizbi.org) funded by NIH & EMBO.

This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO.

Eric Westhof (bit.ly/ewesthof) presents an overview of the use of visualization in studying the 3D structure of RNA molecules. He highlights the compact and elegant visual representation of base-pairing he and others have developed that enable many of the essential features of RNA 3D structures to be represented in 2D. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (vizbi.org) funded by NIH & EMBO. Slides from the talk are at bit.ly/nvudMD.

John Quackenbush (hvrd.me/quakenbush) gives an entertaining and thought-provoking look at developments in the analysis & visualization of high-throughput mRNA data-sets, especially heat-maps. He discusses trends towards centralized repositories, web-based visualization, and highlights the need to better address variance in gene expression, and to better integrate pathways and clinical data. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (vizbi.org) funded by NIH & EMBO. Slides from the talk are at bit.ly/okXOAM.

Yoseph Barash (bit.ly/jbarash) introduces how genes are alternative spliced, highlights limitations in current methods for visualizing splicing data, and speculates on how future methods may evolve. He presents his remarkable 'splicing code', recently published in Nature, which concisely explains tissue-specific splicing regulation. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (vizbi.org) funded by NIH & EMBO. Slides from the talk are at bit.ly/q0KY56.

Tamara Munzner (www.bit.ly/tmunzner) presents very lucid and useful guidelines for creating effective visualizations, including how to correctly rank visual channel types and how to use categorical color constraints. She explains advantages of 2D representation and drawbacks of 3D, immersive, or animated visualizations. She also describes how to create visualizations that reduce the viewer's cognitive load, and how to validate visualizations. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (vizbi.org) funded by NIH & EMBO. Slides from the talk are at bit.ly/nCJM5U

John Westbrook (pdb.org) gives a concise and useful summary of database-oriented structure visualization. He first reviews the types of 3D macromolecular structure data available, the shape classification methods used to categorize and search structures, and the key visualization methods used. He highlights methods that integrate 3D structure visualization with other kinds of biological data and with life science literature. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (vizbi.org) funded by NIH & EMBO.

Arthur Olson (www.mgl.scripps.edu) gives a very engaging demonstration of how molecular recognition and self-assembly can be explored using an innovative, hybrid user interface that combines 3D solid printing and his own augmented reality environment. He argues that a synthesis of both abstract & 3D visualization is needed to understand biological processes. He then presents impressive, cutting-edge methods for fast, integrated, and large-scale macromolecular visualization. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (www.vizbi.org) funded by NIH & EMBO.

Gaël McGill (www.bit.ly/pmgxqF) introduces key visualization methods used to study macromolecular dynamics, finishing with several stunning, narrative-driven visualizations created by tools such as BioBlender, ePMV, and Molecular Maya. He highlights the current lack of sharing of molecular meta-models as a key challenge impeding progress, and discusses the need to bring macromolecular dynamics into education. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (www.vizbi.org) funded by NIH & EMBO.

Trey Ideker (http://www.idekerlab.ucsd.edu) discusses methods for visualizing high-throughput protein-protein and protein-DNA interaction data, which often produce the infamous 'hairballs'. He presents several compelling examples, using the widely-used Cytoscape tool he founded, that demonstrate how network comparison and other methods focusing on biological or bio-medically relevant questions can identify sub-networks that are easily manageable. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO.

Nicholas Luscombe (http://www.bit.ly/nluscombe) gives a lucid and thorough account of how his group studies transcriptional regulation using primarily four visualization methods: genome browsers, heat-maps, networks, and 3D spatial visualization. He identifies three key challenges: (1) integration, particularly switching between visualizations; (2) managing new information types such as quantitative data, dynamics, & population variability; (3) communicating complex data to peers. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO

Susumu Goto (http://www.bit.ly/olXYKt) gives a clear outline of the computer-assisted - but substantially manual - methods his group use to construct the metabolic network visualizations behind the widely-used KEGG resource. He demonstrates how these visualizations help in functional interpretation of omics data, allow network comparison across multiple species, and can predict new pathways, including non-metabolic networks. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO.

Yannis Kalaidzidis (http://www.bit.ly/q2dm1Y) explains the 'inverse problem' of high-throughput cellular imaging, i.e., how to transform raw images into abstract visualizations that give insight into biological processes. He gives a clear, concise account of several common strategies, especially profile plots and 2D clustering of phenotypic data, and concludes that high-throughput and multidimensional phenotypic data will remain an ongoing visualization challenge. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://wwww.vizbi.org) funded by NIH & EMBO.

Drew Berry (http://www.bit.ly/drew_berry) explains principles for engaging the public, and shows spectacular highlights of his videos on the malaria life cycle at the cellular scale, on DNA replication, and on the human brain at the tissue, cell, and molecular scale. Drew Berry is one of the world's foremost biomedical animators; he is an Emmy award winner and a MacArthur fellow. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO.

Fernanda Viégas (http://www.bit.ly/pgIjPl) and Martin Wattenberg (bewitched.com) present a fascinating selection of scientific and artistic works illustrating diverse approaches to information visualization. These include strategies for showing patterns in data, for enabling navigation in large data-sets, and for making visualizations more engaging, fun, and easier to comprehend. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO.

Willy Supatto (http://www.bit.ly/o9s2sf) presents dramatic 4D image data of embryonic development, and provides a classic case study where a 2D representation provided clear insight into cell division patterns not noticed in the original 4D data. He identifies the lack of specifically-tailored visualization tools as a key challenge for embryonic development research; other challenges include how to combine data from multiple experiments, and how to integrate raw data. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO.

Rob MacLeod (http://www.bit.ly/nFyPvU) highlights the role of visualization in the development of a wide range of medical devices and surgical procedures that his group has been involved with. He identifies several key challenges, including visualization on portable devices, representation of uncertainty, management of very large data-sets, and the sometimes urgent need for speed in medical applications. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO.

Hervé Tettelin (http://www.bit.ly/nydBga) gives a lucid summary of methods for visually comparing genomes across populations, including members of a species, or organisms sharing an environment, such as the human microbiome. He highlights the case of microbial pan-genomes, and discusses many vexing visualization challenges faced in this emerging field, particularly population dynamics. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO. Slides from the talk are at http://www.bit.ly/oH4HjK.

Des Higgins (http://www.bioinf.ucd.ie) gives a very entertaining introduction to the visualization of multiple sequence alignment, and to his widely-used Clustal tool. He highlights the emerging challenge of managing alignments with a very large number of sequences, and presents several approaches to this challenge, including faster algorithms and abstract views of clusters of alignments. This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO.

Rod Page (http://www.bit.ly/qW3Len) gives an engaging and forward-looking talk on the visualization of phylogenies, highlighting many limitations of the commonly-use tree metaphor by contrast with geographical maps. He highlights the emergence of geophylogenies, which combine trees and maps, and predicts an increased role for touch screen interfaces and for methods that enable rapid zooming between different scales (e.g., Zoomify). This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO.

This talk was presented at VIZBI 2011, an international conference series on visualizing biological data (http://www.vizbi.org) funded by NIH & EMBO.