Call for Participation

Poster poster submitters please note: A shorter version of the CFP specifically for abstract submissions is available here.

(1) Aims and Scope

The rapidly expanding field of biology creates enormous challenges for computational visualization techniques for enabling researchers to gain insight from their large and highly complex data sets.
The goal of the Symposium on Biological Data Visualization (BioVis) is to establish a premier international and interdisciplinary event for all aspects of visualization in biology. The Symposium aims at bringing together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in problems in biological data visualization as well as bioinformatics and biology researchers in state-of-the-art visualization research.
The symposium will serve as a platform for researchers from these fields to increase the impact of visualization approaches in biology. The breadth and diversity of biological research topic areas will enable researchers from all parts of the visualization community to contribute to this effort and the symposium will provide an excellent opportunity to initiate interdisciplinary collaborations. Finally, it will provide an outlet and training ground for young and freshly minted visualization researchers with a keen interest in problems of biology and provide a venue for researchers in biology and bioinformatics to share pressing visualization challenges and potential solutions in their fields.

(2) Topics

We are looking for contributions on all aspects of visualization in biology. Suggested topics include, but are not limited to:

  • Genome and sequence data, including genomic variation data
  • Multivariate omics data (transcriptomics, proteomics, metabolomics, etc.)
  • Phylogenetic data
  • Biological networks and pathways
  • Biological Ontologies
  • Structures (e.g., protein or RNA structures)
  • Visualization of image data, such as microscopy or radiological data
  • Integration of image and omics data for systems biology
  • Modeling, simulation, and visualization of biological systems
  • Visualization in neurobiology and developmental biology
  • Systems and software frameworks for biological visualization
  • Integration of visualization in biological workflows or collaborative processes
  • Visualization and visual analytics of integrated data sets
  • Usability of visualization by biologists
  • Creation and visualization of biological atlases and metadata
  • Processes for interdisciplinary collaboration between biology and visualization.
  • Visualization and visual analysis of eQTL data (see related information on the Contest web page on http://www.biovis.net)

(3) Symposium Format

The symposium will be a two-day single-track event with keynote and invited talks, papers sessions, contest entries presentation, panels, and posters/demos. Tutorial sessions, in the form of primers, for  bioinformatics, biology, and visualization researchers will be organized.

(4) Submission Types and Criteria

Given the goal of bringing together members of the both the biology and visualization communities for discussion, the symposium solicitation is purposefully broad and open minded to diverse types and lengths of submissions. Authors are encouraged to self identify the intent of their submission. Each paper will be handled in the review process and given appropriate time and venue at the symposium in accordance with its stated intent and length. Types of submissions include, but are not limited to:

  • Detailed reports of original research
  • Highlights about relevant previously published work with some additional insight
  • Descriptions of work in progress and preliminary results
  • Experience reports
  • Demonstrations of new systems, perhaps including distribution of working code
  • Descriptions of analysis challenges of a newly published dataset, potentially as a challenge to the visualization community to help produce solutions

Authors should indicate the intended publication type of their submissions, as one of three categories:

  • Papers: Up to 8 page papers describing high quality research that is not necessarily fully completed but offers some new insight. Selected papers will have an opportunity for an extended and refined invited follow-up submission (see Section 9). Authors will have an oral presentation in a session with an emphasis on discussion with the audience.
  • Posters: Submissions consist of an up to 2 page extended abstract summarizing the authors’ work. Posters are meant to support an exchange of ideas and can be based on work-in-progress. Authors must present a corresponding poster during the designated poster session, and are encouraged to incorporate a demo or video into their presentation. All authors have the opportunity to give a brief oral preview during a plenary “fast forward” session. Authors of selected posters will be invited to provide a longer oral presentation at the symposium.
  • Contest Entries: Submissions consist of an up to 4 page extended abstract summarizing the contest entry. Supplementary material is also welcome in form of Powerpoint slides, software virtual box images and/or binary distributions, technical reports, and supporting manuscripts. A subset of selected contestants will have the opportunity to present their work in a separate session during the symposium. 

More information about each category of content and the various submission guidelines can be found on the submission page.

(5) General Expectations (Ethics Guidelines)

At least one author of an accepted submission must attend the conference to present the work. When submitting your paper you will be asked to provide a complete list of authors even when submitting an anonymized version of the manuscript. This is required to avoid potential conflicts of interest when assigning reviewers. Adding additional authors AFTER the acceptance of a paper is unacceptable and will not be permitted.

All submissions will be treated as confidential communications during the review process, so submission does not constitute public disclosure of any ideas therein. Submissions should contain no information or materials that will be proprietary or confidential at the time of publication (at the conference), and should cite no publications that are proprietary or confidential at the time of publication.

Authors of poster entries will also abide by similar guidelines. Any use of copyrighted material and devices of proprietary nature will be the responsibility of the presenters.

Contestants will also use the contest data in the spirit of academic collaboration and inquiry. The use of patented and proprietary solutions and software will be permitted for demonstrating the results in a forum at the Symposium. However, it is encouraged that the final submission include open-source code distribution and anonymized data to foster academic collaborations.

Our symposium will adhere to the VGTC ethics guidelines for reviewers that can be found at http://vgtc.org/wpmu/techcom/conferences/ethics-guidelines/.

(6) Review Process

Reviewers from both visualization and bioinformatics communities will be involved in the review process. Paper and poster submissions will be evaluated by external reviewers organized by the Papers and Posters Chairs, respectively. Papers will be reviewed for novelty and contribution, while posters will be considered for their quality and value to the symposium audience. Contest entries will be judged for their contribution to the state-of-the-art in visualization, and in their ability to provide biological insights. The review committee for the contest entries will draw upon the existing BioVis reviewers while recruiting others from various pertinent research communities in biology and bioinformatics.

(7) Important Dates

  • Paper submission: Monday, April 30, 2012 
    Notification of acceptance of papers: Thursday, June 20, 2012
  • Poster Entry submission: Wednesday, June 27, 2012
    Notification of acceptance of posters: Friday, July 27, 2012 
  • Contest Entry submission: Wednesday, July 11, 2012
    Notification of acceptance of contest entries: Friday, July 27, 2012
  • Camera ready copy: Saturday, August 25, 2012 
    Extended Journal Format Submission: TBD

All deadlines are at 5:00pm Pacific Time (PDT).

(8) Supplemental Material and Formatting Guidelines

Paper and poster submissions can include full-color figures throughout. We encourage the use of digital video to enhance the submission, particularly if part or all of the work addresses interactive techniques. Submission of working code and other supplemental material in order to increase the reproducibility of the work is also encouraged. The material for the contest entries should include all of the aforementioned content. It will be however, advantageous to include all material which will convince the reviewers of the specificity and topicality of the offered solutions. Open-source software should be included for all contest entries. If open-source solutions cannot be included, the contestants should provide sufficient rationale while providing an appropriate collection of binaries and executables.

The review process for the paper track will be optionally double-blind for those who want to submit their work anonymously. When submitting for double-blind reviewing you are asked NOT to include any identifying information in the submission. Otherwise, the review process will be single-blind, i.e. the reviewers know the identity of the authors, but the authors do not know the identity of the reviewers.

Links to details and guidelines for preparing a proper submission and supplementary data can be found on the submission page. Authors must follow the style guidelines specified therein.

(9) Publications

The symposium proceedings will consist of all accepted papers and will appear in the IEEE Digital Library. Accepted poster and contest submissions will be included in the electronic conference proceedings and made available on the symposium website.

To increase the visibility of visualization within the bioinformatics and biology communities, a selection of the best accepted papers and contest entries will be invited to be published in expanded form in an open-access, peer-reviewed bioinformatics journal such as BMC Bioinformatics.

(10) Submission

Details on how to submit papers, posters and contest entries are provided on the submission page.

(11) Paper, Contest, and Poster Awards

Best paper and poster prizes will be awarded. Submissions that resulted from a successful collaboration between researchers from both the visualization and biology communities will be especially regarded. Reviewers will be queried on the review form with a question "Should we consider this paper/poster for the best paper/poster award? (yes/no/maybe)". Contest entries will be rewarded for creating either the best visualization among the competing entries, or for gleaning the most biological insights. Another prize will be awarded for best overall entry.

Call for Posters

1. Symposium Aims and Scope

The goal of the Symposium on Biological Data Visualization (BioVis) is to establish a premier international and interdisciplinary event for all aspects of visualization in biology. This Symposium aims at bringing together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in biological data visualization, as well as bioinformatics and biology researchers in state-of-the-art visualization research.

2. Poster Topics

We are looking for contributions on all aspects of visualization in
biology. Suggested topics include, but are not limited to:

  • Genome and sequence data, including genomic variation data 
  • Multivariate omics data (transcriptomics, proteomics, metabolomics, etc.) 
  • Phylogenetic data 
  • Ecological and taxonomic data 
  • Biological networks and pathways 
  • Biological Ontologies 
  • Sructures (protein structures, RNA structures, etc.) 
  • Subcellular, cellular, tissue- and organ-level structures 
  • Visualization of image data, such as microscopic or radiological data 
  • Integration of image and omics data for systems biology 
  • Modeling, simulation and visualization of biological systems 
  • Visualization in neurobiology and developmental biology 
  • Systems and software frameworks for biological visualization 
  • Integration of visualization in biological workflows or collaborative processes 
  • Visualization and visual analytics of integrated data sets 
  • Usability of visualization by biologist 
  • Creation and visualization of biological atlases and metadata 
  • Processes for interdisciplinary collaboration between biology and visualization 
  • Visualization and visual analysis of eQTL data (see related information on the Contest web page) 

3. Poster Criteria

Given the goal of bringing together members of both the biology and visualization communities for discussion, the symposium solicitation is purposefully broad and open-minded to diverse types of submissions. The posters are meant to support an exchange of ideas and can be based on work-in-progress. Although submissions may present relevant research previously published for a different community (e.g. a biology or bioinformatics conference or journal), we will not accept material submitted simultaneously to another VisWeek 2012 venue.

Each extended abstract will be reviewed by the Program Committee. Types of submissions include, but are not limited to:

  • Descriptions of work-in-progress and preliminary results 
  • Demonstrations of new or recent systems, both open source and proprietary 
  • Descriptions of analysis challenges where current tools fall short for  specific datasets and goals to inform the visualization community in producing better future solutions 
  • Ideas for future research directions 
  • Experience reports, highlighting lessons learned from the deployment of relevant previously published work
  • Reports of original research 

Poster submissions consist of an extended abstract (up to 2 pages), which may include figures. Do NOT submit the actual large format poster document. Accepted submissions will be presented as posters at the Symposium and we encourage authors to include a demo or video into their presentation. All presenters will have the opportunity to give a brief overview of their work in a plenary "fast-forward session". Presenters of selected posters will be given the opportunity for longer oral presentation at the Symposium.

All extended abstracts will be considered a "personal communication" to the symposium attendees. The extended abstracts will not be published in the proceedings, but will appear in the program, with the distributed Symposium materials, and on the Symposium website.

4. Important Dates

Poster extended abstract submission: Wednesday, June 27, 2012
Notification of acceptance: Friday, July 27, 2012

Camera ready copy: Saturday, August 25, 2012

All deadlines are at 5:00 pm Pacific Time (PDT).

Details on how to submit Poster extended abstracts are provided on the Submission page. 
 

Contest

See also the contest forum for additional information.

The biological domain for the 2012 contest is a continuation of the expression Quantitative Trait Locus (eQTL) analysis problem from BioVis 2011. eQTL experiments catalog massive collections of correlated genotype and phenotype data, with the goal of detecting and identifying important genome-sequence variations that affect phenotypic (specifically RNA expression level) outcomes through non-obvious mechanisms. Typically these mechanisms involve networks of interacting polymorphisms that non-linearly affect specific gene expression levels and are conditional on the presence of other polymorphisms, and the underlying tissue type. Two simultaneous challenges are being proposed.

  • Metadata Challenge - This introductory challenge (Phase I, to be continued in 2013) asks for effective visualizations to identify medically relevant and salient single nucleotide polymorphisms (SNPs) of given eQTL data by leveraging metadata in existing databases.
  • expression Quantitative Trait Locus (eQTL) Challenge - This advanced challenge (Phase II, continuation of Biovis 2011 Contest) solicits visualization solutions o to identify the association patterns of genome-sequence variations, and expression-levels, that predict the occurrence of Tristram's Syndrome (a hypothetical disease around which the data was synthesized).

The base data set for both challenges this year is a data set describing a set of individuals and their genotypes, and their gene expression levels as assayed for several genes. The two visualization challenges examine this data from different perspectives. For contestants who may wish to focus purely on a visual representation, rather than develop an interactive approach that requires analysis or a combination of visualization and analysis, we provide partial analyses of the base data set. These include a partial catalog of metadata for the Metadata Challenge, and single and two-locus PLINK results for the eQTL Challenge.

Visit the contest forum for announcements, additional background on the challenges and biological domain or to just ask questions.

Metadata Challenge

Main Challenge

Using the eQTL data provided, provide visualizations that help researchers take advantage of these databases to identify the SNPs in the eQTL data that are most likely to have a medically relevant, or at least causal, effect, and present this information usefully - in effect, "tell the story" of the how, and why, the patterns of SNP polymorphisms affect phenotypic gene variation. It is possible that several SNPs will have related effects, which reinforces the likelihood that they are important. We will periodically release suggestions and hints regarding important features that you may want to consider in your visualization, via the Contest Forum.

Expression Quantitative Trait Locus (eQTL) Challenge

Main Challenge

Using the data provided, identify the pattern of genome-sequence variations, and expression-levels, that predict the occurrence of Tristram's Syndrome (a hypothetical disease around which the data was synthesized). To as great an extent as possible, elucidate and explain these factors, and the pattern of interaction amongst the factors, influencing the incidence of Tristram's Syndrome. The factors that have been built into the data include both direct SNP effects on the genes that contain them (cis effects), SNP effects on distant genes (trans effects), networks of cis and trans-acting SNPs, and gene-gene interactions.

Mini Challenges

Contestants may also choose to tackle smaller subsets of the data for their entry. The three classes of gene (cell-cell adhesion, serotonin and dopamine) each provide independent information about the disease (though this ignore the interactions across gene classes). Contestants may choose to focus on one of these gene families.

Both main and mini challenge entries will be judged on how well they address the following:

  1. Identification of the most important genes for predicting Tristram's Syndrome from the brain gene expression values.
  2. Identification of the SNPs within those genes that influence gene expression.
  3. Examination of the blood gene expression values to see what could be detected in a simple blood sample, and determine the predictive power of a blood sample for predicting disease. This last criterion is the most important, however, to judge the correctness of the process that lead to the prediction from blood, the first two criteria must be fully documented.

As an optional bonus challenge, contestants may build a predictive statistical model and provide the percent accuracy their model has in predicting disease.

Submissions and Judging

Submissions consist of an up to 4 page extended abstract summarizing the contest entry. Supplementary material is also welcome in form of slide decks (PDF format), virtual machine images and/or binary distributions, technical reports, and supporting manuscripts. A subset of selected contestants will have the opportunity to present their work in a separate session during the symposium.

Contest entries will be judged for their contribution to the state-of-the-art in visualization, and in their ability to provide biological insights. The review committee for the contest entries will draw upon the existing BioVis reviewers while recruiting others from various pertinent research communities in biology and bioinformatics.

Timeline

March 7th Contest Announcement and data release
April 30th Paper submissions due - Contest entries can be submitted as papers
June 27th Poster submissions due - Contest entries can be submitted as posters
July 11th Contest entry submissions due
July 27th Notification of acceptance of contest entries and poster submissions
August 25th Camera-ready submission of accepted Biovis papers
October 15th Contest winners announced at Biovis 2012!

Contacts

Contest General Address contest@biovis.net
Contest Chairs Christopher Bartlett, Raghu Machiraju, William Ray
Meta Data Challenge Data Providers
and Domain Experts
Larry Hunter, Benjamin Keller
eQTL Challenge Data Provider
and Domain Expert
Christopher Bartlett
Contest Forum Forum, Moderator - William Ray

 

Submission

Please see Call for Participation for details about submission types and criteria.

Please prepare your submissions (paper and/or poster abstract) according to the instructions for IEEE Visualization & Graphics Technical Committee (VGTC) conferences. LaTeX and Microsoft Word templates are provided. Please note that the instructions for InfoVis and Vis papers are not relevant for submissions to BioVis.

Guidelines for the preparation of camera-ready papers (after acceptance) are also located on the website of the IEEE Visualization & Graphics Technical Committee.

Paper Upload

BioVis 2012 is using the PCS submission system for paper submissions.

  • To submit a paper go to https://precisionconference.com/~vgtc, log in, and select "Submit to BioVis 2012 Papers". Remember that all materials have to be submitted by April 30, 5 PM PDT. Authors will be notified about the decision of the Program Committee by June 20.

Poster Upload

BioVis 2012 is using the PCS submission system for poster submissions.

  • To submit an poster abstract go to https://precisionconference.com/~vgtc, log in, and select "Submit to BioVis 2012 Posters". Remember that all materials have to be submitted by June 27, 5 PM PDT. Authors will be notified about the decision of the Program Committee by July 27.
  • Poster submissions consist of an extended abstract (up to 2 pages), which may include figures. This should be formatted according to the IEEE VGTC guidelines described above under "submission". Do NOT submit the actual large format poster document.

Contest Upload

All materials have to be submitted by July 11, 5 PM PDT. Authors will be notified about the decision of the Program Committee by July 27. Detailed information can be found on the contest page. 

Registration

Registration for BioVis 2012 is handled through the IEEE VisWeek 2012 registration system:
http://visweek.org/visweek/2012/info/registration/conference-registration

 
One day and two day registrations is available.

Organizing Committee

General chairs

Paper chairs

Poster chairs

Publication chairs

Primer/tutorial chairs

Challenges chairs

Contest chairs

Industry and fundraising chairs

Website and publicity chairs

Steering committee

Program committee

The BioVis 2012 international program committee will include both visualization and bioinformatics scientists from a wide range of domains.

  • Aerts, Jan, KU Leuven, Belgium
  • Anshus, Otto, University of Tromsø, Tromsø, Norway
  • Bejerano, Gill, Stanford, USA
  • Bertini, Enrico, University of Konstanz, Germany
  • Blake, Judith, The Jackson Laboratory, USA
  • Botha, Charl, Delft University of Technology, Netherlands
  • Bruckner, Stefan, Vienna University of Technology, Austria
  • Carter, Greg, The Jackson Laboratory, USA
  • Dubchak, Inna, Lawrence Berkley Laboratory, USA
  • Duke, David, University of Leeds, UK
  • Dunham, Maitreya, University of Washington, USA
  • Durand, Dannie, Carnegie Mellon University, USA
  • Görg, Carsten, University of Colorado, USA
  • Graber, Joel, The Jackson Laboratory, USA
  • Gresham, David, New York University, USA
  • Hege, Hans-Christian, Zuse-Institute Berlin, Germany
  • Hibbs, Matthew, The Jackson Laboratory, USA
  • Hunter, Larry, University of Colorado, USA
  • Huson, Daniel, University of Tübingen, Germany
  • Huttenhower, Curtis, Harvard School of Public Health, USA
  • Johnson, Chris, University of Utah, USA
  • Joshi, Alark, Boise State University, USA
  • Jurisica, Igor, Ontario Cancer Institute, Canada
  • Kennedy, Jessie, Edinburgh Napier University, UK
  • Kingsford, Carl, University of Maryland, USA
  • Lappe, Michael, Max Planck Berlin, Germany
  • Linsen, Lars, Jacobs University, Germany
  • Möller, Torsten, Simon Fraser University, Canada
  • Müller, Heimo, Medical University of Graz, Austria
  • Markowetz, Florian, University of Cambridge, USA
  • Marshall, David, James Hutton Institute, UK
  • Merhof, Dorit, University of Konstanz, Germany
  • Meyer, Miriah, University of Utah, USA
  • Morris, Scooter, UCSF, USA
  • Myers, Chad, University of Minnesota, USA
  • Nieselt, Kay, University of Tübingen, Germany
  • Preim, Bernhard, University of Magdeburg, Germany
  • Ray, William, The Ohio State University, USA
  • Rockman, Matt, New York University, USA
  • Roerdink, Jos, University of Groningen, The Netherlands
  • Ropinski, Timo, Linköping University, Sweden
  • Schneider, Reinhard, EMBL Heidelberg, Germany
  • Schreiber, Falk, IPK Gatersleben, Germany
  • Singh, Mona, Princeton University, USA
  • Streit, Marc, Johannes Kepler University Linz, Austria
  • Trutschl, Marjan, Louisiana State University, USA
  • van Hijum, Sacha, Radboud University Nijmegen Medical Centre, The Netherlands
  • van Liere, Robert, CWI Amsterdam, Netherlands
  • Weber, Gunther, Lawrence Berkeley National Lab, USA
  • Westenberg, Michel, Technical University Eindhoven, The Netherlands
  • Wiebel, Alexander, Zuse Institute Berlin, Germany
  • Ynnerman, Anders, Norkoping University, Sweden
Schedule

All BioVis sessions except the poster viewing will take place in Ballroom C on the 2nd Floor. Posters will be set up in the 2nd Floor Foyer. The VisWeek program contains a map of the location.

  Sunday
08:30 Welcome & Keynote Session
Christof Koch: Project MindScope
10:10 Coffee Break
10:30

Paper Talks 1 - Neurobiology
Chair: Hans-Christian Hege

Neurobiology Primer Talk*: Christopher Bartlett, The Ohio State University, USA

Interactive Extraction of Neural Structures with User-Guided Morphological Diffusion
INCIDE the Brain of a Bee: Visualising Honeybee Brain Activity in Real Time by Semantic Segmentation
Towards real-time visualization of detailed neural tissue models: view  frustum culling for parallel rendering
Visualization of Serial Electron Microscopy Images Using Local Variance

12:10 Lunch Break
02:00

Paper Talks 2 - Systems Biology and Omics Data
Chair: Larry Hunter

Systems Biology and Omics Data Primer Talk*: Cydney Nielsen, British Columbia Cancer Agency Genome Sciences Centre, Canada

MaTSE: The Microarray Time-Series Explorer
Gene-RiViT: A visualization tool for comparative analysis of gene neighborhoods in prokaryotes
ADVISe: Visualizing the dynamics of enzyme annotations in  UniProt/SwissProt
Heterogeneity-based Guidance for Exploring Multiscale Data in Systems Biology

03:40 Coffee Break
04:15

Poster Talks & Poster Fast Forwards
Chairs: Cydney Nielsen and Robert Kincaid 

StratomeX: Enabling Visualization-Driven Cancer Subtype Analysis
Visualization and Exploration of 3D Toponome Data
compreheNGSive: A Tool for Exploring Next-Gen Sequencing Variants
MedSavant: Visual Analytics for Genetic Variation Datasets

05:30 Break
06:00 Poster Session and Reception (until 7:30)
  Monday
08:30

Paper Talks 3 - Cellular Data
Chair: Lars Linsen

Cellular Data Primer Talk*: Larry Hunter, University of Colorado, USA

mzRepeat: Visual Analysis of Lipids in Mass Spectrometry
Epithelial Cell Reconstruction and Visualization of the Developing Drosophila Wing Imaginal Disc
Similarity Analysis of Cell Movements in Video Microscopy
Visualizing Cells and their Connectivity Graphs for CompuCell3D

10:10 Coffee Break
10:30

Paper Talks 4 - Biomolecular Data and Pathways
Chair: Kay Nieselt

Biomolecular Data and Pathways Primer Talk*:  Igor Jurisica, Ontario Cancer Institute, Canada

Dynamic Channels in Biomolecular Systems: Path Analysis and Visualization
Uncertainty-Aware Visual Analysis of Biochemical Reaction Networks

enRoute: Dynamic Path Extraction from Biological Pathway Maps for In-Depth Experimental Data Analysis
Implicit Surfaces for Interactive Graph Based Cavity Analysis of Molecular Simulations

12:10 Lunch Break
02:00 Contest  and Community Session
03:40 Coffee Break
04:15 Challenges Session
Inna Dubchak: Key Challenges with Genome & Population Data
Valerie Daggett: Key Challenges with Visualising Macromolecules
05:30 Awards Ceremony & Closing Remarks (until 5:55 pm)
   

* All paper sessions start with a Primer Talk to introduce the biological background and major domain challenges that are relevant to the papers presented in that session. Primer Talks are aimed at a general audience to make the BioVis paper presentations more accessible to visualization researchers without a background in biology.

Speakers

Keynote

Project MindScope

The Allen Institute for Brain Science has initiated a ten year project to study the principles by which information is encoded, transformed and represented in the mammalian cerebral cortex and related structures. The Institute will build a series of brain observatories to identify, record and intervene in the neuronal networks underlying visually guided behaviors in the mouse, including visual perception, decision making and consciousness. This is a large-scale, in-house team effort to synthesize genomic, anatomical, physiological and theoretical knowledge into a description of the wiring scheme of the cortex, at both the structural and the functional levels. I will describe the associated computational and informatics challenges. The fruits of this cerebroscope will be freely available to the public.

Christof Koch

Christof Koch, PhD
Chief Scientific Officer, Allen Institute of Brain Science


Born in the American Midwest, Christof Koch grew up in Holland, Germany, Canada, and Morocco, where he graduated from the Lycèe Descartes. He studied Physics and Philosophy at the University of Tübingen in Germany and was awarded his Ph.D. in Biophysics in 1982. After four years at MIT, Dr. Koch joined Caltech in 1986, where he is the Lois and Victor Troendle Professor of Cognitive and Behavioral Biology. In 2011, he became the CSO of the Allen Institute of Brain Science in Seattle to lead a large scale, focused and high-throughout, ten year effort to understand coding in the visual neocortex. The author of more than three hundred scientific papers and journal articles, patents and books, Dr. Koch studies the biophysics of computation, and the neuronal basis of visual perception, attention, and consciousness. Together with Francis Crick, with whom he worked for 16 years, he is one of the pioneers of the neurobiological approach to consciousness. His latest book is Consciousness: Confessions of a Romantic Reductionist (MIT Press, 2012).

Challenges Session

We have selected a range of speakers that, together with the keynote speaker, will cover developments in a broad range of active research topics in modern biological data visualization, from genes to proteins to organisms to populations. The speakers include developers of visualization tools widely used in biology, as well as active users who apply visualization methods to discover new biological knowledge.

Key Challenges with Genome & Population Data

As our ability to generate huge amounts of sequencing data continues to increase, data analysis is becoming the rate-limiting step in genomics studies. There are a number of graphical methods designed for the analysis of genome assemblies, genome browsing, comparative genomics, etc. Visualization tools facilitate analysis tasks by enabling researchers to explore, interpret, and manipulate their data. We will highlight new challenges in visualization that are not only a consequence of the sheer volume and complexity of genomic data, but also its increasing utility outside genomics research. Traditional genome visualization approaches do not meet the needs of emerging fields such as medical genomics and metagenomics, and new paradigms are needed.

Inna Dubchak

Inna Dubchak, PhD
Staff Scientist, Genomics Division and Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory


Born in Moscow, Dr. Dubchak was awarded her Ph.D. in Physics with emphasis on Crystallography and Computational Methods by the Russian Academy of Sciences. In the 1990’s, during her postdoctoral training at the University of California in Berkeley, she quickly realized the potential of the emerging study of genomic data and switched to the fields of computational biology and bioinformatics. Since then, she has authored more than 100 academic articles and led a group that focuses on the analysis, organization, and visualization of large volumes of genomics information. Her team has developed a number of excellent visualization tools, including the VISTA family of programs for comparative genomics, which has become one of the major systems used by the biological community. The international popularity of the tools developed by Dr. Dubchak’s lab can be attributed to innovative features, exceptionally user-friendly and modern interfaces, and meticulous attention to biological details.

Key Challenges with Visualising Macromolecules

This talk will give an overview of key challenges emerging in visualizing macromolecule structures, and especially in the representation, navigation and usage of data from high-throughput macromolecular dynamics simulations.

Valerie Daggett

Valerie Daggett, PhD
Professor of Bioengineering and Adjunct Professor of Biochemistry, Biomedical & Health Informatics, University of Washington


Valerie Daggett is Professor of Bioengineering, and Adjunct Professor of Biochemistry, Biomedical & Health Informatics at the University of Washington (Seattle, WA, USA). She holds a B.A. from Reed College and a Ph.D. from the University of California, San Francisco. Prior to her current appointment, she was a postdoctoral Fellow at Stanford University (1990-1993). Current Research Focus: "Our goal is to perform realistic molecular modeling studies relating to protein stability, function, and folding. Protein folding is one of the fundamental unsolved problems in molecular biology. A protein must assume a stable and precisely ordered conformation to perform its biological function properly. Although much is known of the structural details of the native folded conformation of proteins, very little is known about the actual folding process. An understanding of protein folding has important implications for all biological processes, including protein degradation, protein translocation, aging, and human diseases, including cancer and amyloid diseases. The solution to the protein folding problem also has applications in the human genome project and biotechnology. Given that protein folding is of such widespread importance to human health and the fact that experimental approaches only provide limited amounts of information on the structural transitions and interactions occurring during protein folding, we are using computer simulation methods in an attempt to delineate the important forces acting during this process. We have also become involved in biomaterial and biosensor design, making use of what we have learned in our structural, dynamics, and folding studies of well-studied globular proteins. Other areas of interest include: structural and dynamical consequences of amino acid mutations, hydrophobic hydration, force field and software development, and dynameomics.

 

Presenter Information

We have prepared BioVis slide templates, which are available in light and dark for both normal and widescreen displays. Projectors at BioVis will support both formats. More details about projection and AV are available on the VisWeek website.

About

The rapidly expanding application of experimental high-throughput and high-resolution methods in biology is creating enormous challenges for the visualization of biological data. To address these challenges, researchers in the visualization and bioinformatics communities need to engage in the design, implementation, application, and evaluation of novel visualization techniques and tools that provide insight into large and highly complex data sets.

BioVis 2012 - the 2nd IEEE Symposium on Biological Data Visualization - aims at bringing together researchers from the visualization, bioinformatics, and biology communities to establish an interdisciplinary dialogue and to promote the sharing of expertise, between both meeting participants and the communities at large. The meeting is intended to educate, inspire, and engage visualization researchers in problems in biological data visualization, as well as bioinformatics and biology researchers in state-of-the-art visualization research.

The symposium will serve as a platform for researchers from these fields to increase the impact of data visualization approaches in biology. The breadth and diversity of biological research topic areas will enable researchers from all parts of the visualization and bioinformatics communities to contribute to this effort and the symposium will provide an excellent opportunity to initiate interdisciplinary collaborations.

BioVis 2012 will be taking place on 14-15 October 2012 in Seattle, WA and will be co-located with IEEE VisWeek 2012. IEEE VisWeek is the premier forum for visualization advances for academia, government, and industry, bringing together researchers and practitioners with a shared interest in tools, techniques, technology, and theory.

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