Call for Participation

(1) Aims and Scope

The rapidly expanding field of biology creates enormous challenges for data visualization techniques that enable researchers to gain insight from their large and highly complex data sets.
 
The international Symposium on Biological Data Visualization (BioVis) is an interdisciplinary event covering all aspects of visualization in biology. The Symposium brings 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.
 
We invite submissions of original research articles, poster submissions, as well as submissions for data visualization and redesign contests.
 

(2) Topics

We are looking for contributions on all aspects of visualization in biology, from molecular to cell, tissue, organism and population biology. Suggested topics for paper and poster submissions 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)
  • Biological image data, such as microscopy data
  • Integration of image and omics data for systems biology
  • Modeling and simulation of biological systems
  • Neurobiology and developmental biology
  • Systems and software frameworks 
  • Biological workflows or collaborative processes
  • Usability of visualization by biologists
  • Biological atlases and metadata
  • Processes for interdisciplinary collaboration between biology and visualization.
 
The topic of the Data Analysis, and Redesign Contests, is the visualization and analysis of complex networks derived from resting-state fMRI (rsfRMI). Such data define networks that possess physical locations, have physical connectivity that differs from physical proximity, and informational or functional connectivity that differs from both physical layout and physical connectivity.  The contests focus on how to better represent this data, so as to improve the utility of rsfMRI. For more details see http://biovis.net/year/2014/info/contest.
 

(3) Submission Types and Criteria
The symposium seeks submissions in four categories:

The symposium seeks submissions in four categories:
  • Papers: manuscripts describing high quality research.  Manuscripts accepted at the symposium will be published in the symposium proceedings and will be presented orally at the symposium. Accepted papers will also be eligible for a journal publication, for details see Section 9 below. Example manuscripts include, but are not limited to:
  • Detailed reports of original research
  • Description of new systems
  • Evaluation of existing systems or approaches
 
  • Posters: Submissions consist of a brief 250-word abstract and supporting image that summarize the authors’ work. 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.  Example topics include, but are not limited to:
  • Work in progress and preliminary results
  • Previously published work from other venues
  • Visualization challenges relevant to the BioVis community
 
  • Data Analysis Contest Entries: Submissions consist of several parts.  These include: (1) a 250-word abstract;  (2) a 2-page extended abstract describing the problem, your approach and results, suitable for evaluating the extendability of the entry into a full manuscript; (3) up to 4 additional free-text pages, summarizing the contestants' answer to the challenge, and methods/approach for producing the answer;  and (4) a presentation (self-running powerpoint, keynote, or movie) demonstrating the approach and/or further explaining the entry.

Supplementary material ranging from runnable demos in virtualbox images, through published manuscripts, is highly encouraged. Submissions dealing with any aspect of the challenge are encouraged.  Data Analysis Contest entries could include, but are not limited to:

  • complete answers to the specific data analysis contest question
  • partial answers to discrete aspects of the question
  • tools that address all, or part of the question, or similar questions in the domain
  • design studies that argue for better representations for the problem, or answer
 
All accepted entries will be eligible for presentation at the symposium, either as short podium talks, or as data analysis contest poster or demo presentations.
Data Analysis Contest entries deemed to make significant contributions will be invited to submit a manuscript to the thematic series on Biological Data Visualization of the journal BMC Bioinformatics, either as individual submissions, or as collaborative works collecting topically related submissions, at the recommendation of the judges.  
By submitting a Data Analysis Contest entry to BioVis, contestants license the submitted materials to BioVis for dissemination and/or use in BioVis promotional materials.
 
  • Redesign Contest Entries: Submissions consist of a redesign of a figure selected by the judges along with a 1-page abstract motivating the methodology behind the redesign. The abstract should include:
  • aspects of the figure identified as needing improvement or clarification
  • justification of encoding and design choices
  • justification of any points of departure from the original 
 
The judges will select a winner and runner-up. A subset of selected contestants will have the opportunity to present their redesign in a session during the symposium, and entries that make significant contributions will be invited to submit a manuscript to the thematic series on Biological Data Visualization of the journal BMC Bioinformatics, in collaboration with the Data Analysis Contest. All accepted entries will be eligible for presentation at the symposium, either as short podium talks, or as Redesign Contest poster or demo presentations.
 
 
More information about each category of content and the various submission guidelines can be found on http://www.biovis.net.
 

(4) Symposium Format

The symposium will be a two-day single-track event with keynote and invited talks, paper sessions, contest and redesign entries presentation, and posters/demos. Primers acting as tutorial introductions to visualization topics will be provided. 
 

(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. 
 
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 paper review process. Paper submissions will be evaluated by external reviewers organized by the Papers Chairs, and will be reviewed for novelty and contribution. 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.
 
Posters will be reviewed for relevance and interest to the BioVis community by the Poster Chairs. 
 
Data Analysis Contest entries will be reviewed for relevance by the Contest chairs.  Accepted entries will be invited to present a contest poster or demo at the symposium.  Accepted entries will further be peer-reviewed for contribution and technical merit by external reviewers from the BioVis Program Committee, and judged for awards by a panel of experts from relevant visualization and biological domains. Judges will evaluate submissions on criteria including, but not limited to accuracy, visualization or biological contribution, and design and usability, and will select "winning" entries, as well as recommend entries for short podium presentations and for invitation to a special issue of a journal. Entrants should note that accuracy will not be the sole determinant of judging, and that significant and novel contributions to specific aspects of, or sub-problems within the overall problem, will be viewed favorably.  Entrants are encouraged to explicitly state their entries' areas of contribution to facilitate appropriate review.
 
Redesign entries will be judged for design that enhances the narrative and makes good use of visual emphasis. 

(7) Important Dates

Paper submission: March 1, 2014
Preliminary notification: April 10, 2014
Revised manuscript submission: May 10, 2014
Final notification: June 1, 2014
 
Camera ready copy: June 15, 2014
 
Poster submission: May 24, 2014
Notification of acceptance of posters: June 1, 2014
 
Data Analysis Contest entry submission:  May 1, 2014
Notification of acceptance of contest entries: June 1, 2014
 
Redesign Contest entry submission: May 1, 2014
Notification of acceptance of redesign entries: June 1, 2014
 
All deadlines are at 5:00 pm Pacific Time (PDT). 

(8) Submission (incl. Supplemental Material and Formatting Guidelines)

Paper submissions can include full-color figures throughout. We encourage the use of digital video to enhance paper and poster submissions, 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. When possible, Open Source software should be provided for contest entries.
 

Links to details and guidelines for preparing a proper submission and supplementary data can be found on http://www.biovis.net. Authors must follow the style guidelines specified therein. 

(9) Publications

All accepted papers for the conference will be linked on the BioVis website (http://www.biovis.net) and will be made available through the IEEE Digital Library.
In addition, all papers accepted for the conference will be considered for publication in the thematic series on Biological Data Visualization of BMC Bioinformatics. Decision about acceptance will be taken by the associate editors (i.e., the BioVis papers and publication chairs) and the BMC Bioinformatics section editor. Final notification about acceptance for the conference as well as the journal will be June 1, 2014.
Authors will be required to meet costs required by BMC for open access; BMC can also provide waivers in cases where authors have troubles meeting these costs. 
 
All accepted poster submissions will be made available on the symposium website.
 
Data Analysis and Redesign Contest entries that are accepted, and deemed to make a significant contribution to the field, will be invited to submit full manuscripts for inclusion in the thematic series on Biological Data Visualization of BMC Bioinformatics. 

(10) Awards

Papers that resulted from a successful collaboration between researchers from both the visualization and biology communities will be especially rewarded. Reviewers will be queried on the review form with a question "Should we consider this paper for the best paper award? (yes/no/maybe)". 
 
Posters will be assessed for rewards by a judging committee during the poster presentation session. 
 
Data Analysis Contest entries will be rewarded for creating either the best visualization among the competing entries, or for gleaning the most biological insights, and for other valuable contributions as identified by the judging panel. 
 
For Redesign Contest entries, the judges will be be looking for a redesign that enhances the narrative and makes good use of visual emphasis. Focus, clarity and simplicity will be favored over extravagance.

(12) Organizing Committee

General chairs

Paper chairs

Poster chairs

Publication chairs

Primer/tutorial chairs

Challenges chairs

Contest chairs

Design contest chairs

Industry and fundraising chairs

Website chairs

Publicity chairs

(13) Steering committee

 

rsquo; work. 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

Data Contest

Update:

Submissions are now open. See the announcement!

Overview

Protein Mutations and their effect on Protein Function

  • Identify "driver" mutations that change function, and "passenger" mutations that are just along for the ride.
  • Develop new tools and new collaborations to help bio/life-science researchers solve pressing questions.
  • Win prizes and get published at BioVis 2013

The 2013 BioVis contest focuses on the domain of protein function, and how protein sequences generate function. In particular, the contest asks whether, from a collection of mutations to a protein, the ones that are important (i.e. that cause the protein's functionality to change) can be segregated from the ones that are unimportant (i.e. that don't appear to affect function). The goal is to develop a visualization tool that can aid the working bio/life-sciences researcher in identifying important mutations within a larger set in a protein, provide biophysical insight into why those mutations affect function, and potentially suggest additional modifications to the protein that could be used to rescue functionality.

Predicting changes in protein functionality based on changes in sequence remains a significant challenge in the biophysical sciences. Despite burgeoning sequence data and an ever-increasing rate of acquisition, in all but the most trivial cases the answer the simple question "is this mutation likely to affect the function of this protein?", remains elusive.

Evolutionary pressure to maintain function has undoubtedly left its signature in the shared and differing properties of orthologous (belonging to differentiated species) proteins across the phylogenetic tree. However, progress in applying this data to predicting changes in function from changes in sequence has largely been stalled for decades, at least in part, due to the current approaches that use amino acid frequencies from a multiple sequence alignment and declare mutations to affect function only if they lie outside the distribution observed in the family.

Functional proteins, however, are 3-dimensional collections of atoms, and their functionality is determined by how reacting partners and substrates "see" them, in terms of electrostatic fields, topology and surface topography. No residue functions in isolation; therefore, it is the concerted biophysical properties of numerous residues that must be evaluated, to make accurate predictions about whether a mutation affects function. Additionally, to complicate matters current canonical approaches evaluate the acceptability of mutations based on their acceptability in the residue distribution of the family, rather than based on their acceptability in the parent protein.

A visualization tool that integrates 3D structural information and biophysical predictions for a protein, with distribution information from the multiple sequence alignment of the family of proteins with the same function, and with network information extractable from the family phylogeny, and that further could show where the characteristics of the parent and mutant either fit, or differed from the family consensus and from each other, would fundamentally improve researchers' ability to deal with questions in this important domain. The 2013 contest provides the sequence of a significantly mutated triosephosphate isomerase (TIM) that has had almost all functionality abolished by mutations towards family consensus, and poses the question, "Which of these mutations cause the functional defect, and what can be done to rescue functionality?".

We welcome entries that attempt to provide a comprehensive solution to the problem, or, those that focus on some discrete albeit different aspects. A discussion forum is available for for inter-contestant communications, and for providing access to domain scientists who can answer questions, or assist with access to the data.

Contact: contest@biovis.net

Awards

The three entries (Team Vis Favorite, Team Bio Favorite, and Overall Best Entry) will at least receive:

  • A presentation slot during the 2013 BioVis awards ceremony.
  • An award certificate for each member of your team.
  • An invitation to extend your submission into a full paper to appear in the BioVis supplement publication

Additional Awards:

Depending on the number of submissions and the reviews, additional awards may be provided, at the judges' discretion, for outstanding or other distinguishing features of entries.

Publications:

All accepted submissions will be published in the BioVis electronic proceedings. We reserve the right to reject submissions that do not conform to these guidelines, that are of poor quality, that make no contribution to the field, or that are not responsive to the contest problem.

Data

Data is available inside the enclosure of a password controlled forum which is available here.

The data consists of the sequence of a functionally defective triosephosphate isomerase mutant (dTIM) (248 residues) , the S. cerevisiae triosephosphate isomerase (scTIM) parent of our defective TIM (also 248 residues), the structure of scTIM (to which dTIM appears similar), raw sequences of all other known TIMs (1.4Mb of sequences), and a hand-curated alignment provided by our domain experts, of the structural core of the TIM family members they consider to be the most relevant, and from which dTIM was designed.
 
Structures for other TIMs can be downloaded from the RCSB Protein Data Bank at by searching for "TIM".
 
Our domain scientists will monitor the forum closely to answer questions about the data, and also to provide instructions and advice for applying several types of additional analyses to these data, in the contest forum.
Rules

The contest is open to everyone except contest organizers, data providers, and judges. We invite participation from individuals and teams, industry or academia. Individuals may participate on more than one team submission, and we'd love to see new collaborations spring up, to address this problem!

Submissions must be formatted according to the guidelines (to be published), otherwise we reserve the right to reject it without review.

Submission

Important dates and submission requirements

Important dates

Submission Deadline: August 2, 2013
Other dates TBA

Judging

Logistics - TBD

Requirements for winning (any of the 3 top entries):
Entering!
Participation at the conference
Presentation during the BioVis plenary session

Tasks

The overall goal is to produce a visualization tool, or visualization, that accurately suggests mutations that can be added to dTIM to rescue functionality, and that ideally aids the user in understanding why those mutations, in particular, were problematic for functionality, while others were innocuous.

We suggest that you consider some of the following when developing your visualization, though of course, these are mere suggestions. If you have better ideas, you are definitely encouraged to pursue them:

  • Agreement with the family consensus - that is, fitting within the residue distribution as defined by other functional members of the family - is almost certainly not a primary requisite for functionality. Our broken dTIM was created by trying to make a particular species variant of TIM fit the consensus better. As a result, comparisons of the parent (S. cerevisiae) to the family consensus, and some representation of the distance between dTIM and its parent, may be more productive than comparisons of dTIM to the family.
  • The functional deficit caused by some problematic mutations in dTIM can be reversed by mutating them back to their parent residue. Others can be reversed by changing _different_ residues that minimize the impact of the residue already present.
  • The extent to which each residue is constrained to a particular identity, or subset of biophysical properties, varies across the protein. This can be considered a sort of uncertainty. Casting this data into the three-dimensional structure may provide insight into what portions of the protein are generally allowed to change, and which are constrained. Because sequence proximity and spatial proximity are only loosely correlated, examining the spatial locations of mutations may provide insight into their likely acceptability in a fashion that cannot be seen by examining the sequence.
  • A mutation, because it changes a subset of the atoms of the protein, also changes the network of which parts of the protein touch what. This can modify, for example, energy transport mechanisms that require passing an electron from amino acid side-chain to side-chain. It can also alter protein flexibility, or the ensemble of conformations that the protein can adopt.
  • Instructions for running molecular dynamics simulations will be provided in the forum, if you would like to examine how the network of contacts might change in the presence or absence of specific mutations, or how mutations affect the way that the network changes when the protein flexes.
  • Any of the structural-biophysical-volume properties of the protein that can be painted onto a sequence or multiple-sequence-alignment view of the protein, will dramatically aid end-users in applying their domain knowledge and intuition to the problem.
  • Any of the multiple sequence alignment properties that can be painted onto the structure, likewise would be quite useful to the working bio/life-sciences researcher.
  • Not all proteins have structures determined for them. Sequence data is much more easily available, enabling more powerful statistical inferences.
  • Evolution has clearly voiced its opinion regarding requirements for functionality, some of the artifacts of which can be found by looking for groups of residues that co-evolve (that is, where one residue changes, others always change with it) within the family. Identifying these groups and displaying their membership on either the multiple sequence alignment, or on the protein structure, could be very informative.
Organizing Committee

General chairs

Paper chairs

Poster chairs

Publication chairs

Primer/tutorial chairs

Challenges chairs

Data contest chairs

Redesign contest chairs

Industry and fundraising chairs

Website chairs

Publicity chairs

Steering committee

Program committee

Aerts, Jan, KU Leuven, Belgium
Bartlett, Chris, The Research Institute at Nationwide Children's Hospital, USA
Bertini, Enrico, NYU, USA
Carter, Greg, Jackson Lab, USA
Chen, Jian, University of Maryland BC, USA
Goerg, Carsten, University of Colorado, USA
Graber, Joel, Jackson Lab, USA
Hege, Hans-Christian, Zuse-Institute Berlin, Germany
Jianu, Radu, Florida International University, USA
Joshi, Alark, Boise State, USA
Jurisica, Igor, University of Toronto, Canada
Kennedy, Jessie, Edinburgh Napier University, UK
Kincaid, Robert, Agilent, USA
Kingsford, Carl, University of Maryland, USA
Lenhof, Hans-Peter, University of Saarbrücken, Germany
Marai, Georgeta-Elisabeta, University of Pittsburg, USA
Melancon, Guy, INRIA Bordeaux, France
Merhof, Dorit, University of Konstanz, Germany
Meyer, Miriah, Harvard University, USA
Meyer, Folker, Argonne National Laboratories, USA
Morris, Scooter, UCSF, USA
Möller, Torsten, Simon Fraser University, Canada
Mueller, Klaus, Stony Brook University, USA
Munzner, Tamara, University of British Columbia, Canada
Myers, Chad, University of Minnesota, USA
Nattkemper, Tim, University of Bielefeld, Germany
Nieselt, Kay, University of Tübingen, Germany
Preim, Bernhard, University of Magdeburg, Germany
Ray, William, The Ohio State University, USA
Roerdink, Jos, University of Groningen, The Netherlands
Ropinski, Timo, Linkoping University, Sweden
Schneider, Reinhard, EMBL Heidelberg, Germany
Schultz, Thomas, Max Planck Institute for Intelligent Systems, Germany
Sharma, Cynthia, University of Würzburg, Germany
Streit, Marc, Johannes Kepler University Linz, Austria
Strobelt, Hendrik, University of Konstanz, Germany
van Liere, Robert, CWI, Amsterdam, The Netherlands
Vilanova, Anna, TU Eindhoven, The Netherlands
Weber, Gunther, Lawrence Berkeley National Lab, USA
Westenberg, Michel, Technical University Eindhoven, The Netherlands
Wiebel, Alexander, Zuse-Institute Berlin, Germany
Yoo, Terry, NIH, USA
Zhang, Song, University of Mississippi, USA

Redesign Contest

Protein Mutation Profiles

The redesign contest recognizes the importance of effective encodings and clear visual communication in display of complex quantitative information. It gives participants the opportunity to develop a practical replacement to the long-standing convention of sequence logos.
 
 

Chairs

BC Cancer Research Centre, Canada
 
Broad Institute, USA
 

Motivation

Effective data visualization requires a complementary combination of appropriate encoding and effective communication. Once you have created a visual form for the information, the final success of your figure will require that your message is presented logically, that patterns given visual focus, and your narrative and navigational annotations are layered clearly but unobtrusively.
 
Data must not simply be shown—it must be shown with purpose.

Contest Challenge

Trying to compare protein subfamilies that are the result of different evolutionary solutions to the same problem is a typical challenge. The sequence logo is the de facto method of visually representing the data. As a long-standing convention, it is ineffective at organizing information and revealing patterns—the visualization is very limited in assisting the experts discover what they’re really after. In other words, it does a poor job in matching salience to relevance [1].
 
The contest figure is a composite sequence logo for all adenylate kinase enzymes and two different sub-families, which have distinctly different requirements for residues
in some of the positions. 
 
Your task will be to improve this figure. Explore new data encodings and presentation schemes.
 
1. Wong, B. Nat Methods 7, 889 (2011).

The Figure

Sequence logos showing the amino acid usage in the adenylate kinase lid (AKL) domain. (A) Across all organisms. (B) from Gram-negative bacteria. (C) from Gram-positive bacteria.
 
The ADK lid domain structure is universally conserved, but is stabilized in the Gram-negatives by a hydrogen bonding network between residues 4, 7, 9, 24, 27, and 29 (and several other residues in some organisms), while the Gram-positives are stabilized by a bound metal ion, tetrahedrally coordinated by the Cysteines at 4, 7, 24 and 27. The identities of several other positions (eg 5, 8, 30, 32) are differentially constrained in each subfamily as well, apparently due to steric requirements of the stabilizing residues.

Submission

The submission will be composed of the redesigned figure and legend along with a one page abstract that describes the motivation of the redesign. The abstract should include
  • aspects of the figure identified as needing improvement or clarification
  • justification of encoding and design choices
  • justification of any points of departure from the original
You are free to leave things out in the redesign, if you feel they are superfluous. Exercise discretion when adding elements to the figure—the original spirit should be intact without adding complexity.
 
You are free to rewrite the legend, but the new version must include all relevant information. Parts of the original legend draw attention to existing features in the data that are important, but difficult to identify in the figure. For example, at position 8 glycine is absolutely conserved in the Gram-negatives, while only strongly in the Gram-positives. This slight difference in preference is only a symptom of a more fundamental difference between the families at this, and other columns (mutual information).
 
The submitted figure size and format must match NPG requirements.
 
Please include the names and affiliations of all submission authors and contact information for the corresponding author.
 

Deadline

2 August 2013

Judging

The judges will be be looking for a redesign that enhances the narrative and makes good use of visual emphasis. The winning participant will have the opportunity to present their redesign in a session during the symposium. All entries will be made available to the participants.
 
Focus, clarity and simplicity will be favored over extravagance.

Terms and Conditions

Given that the nature of this contest is subjective, the judges will provide a short description of the reasoning behind the scoring for each submission. All judges’ decisions are final.
 
By submitting an entry, you give the VIS 2013 and BioVis 2013 organizers permission to publish it in conference-related materials (web site, proceedings, companion papers marketing). Any usage or reference to any submission will include full credit to its authors.

Download

The contest package includes the figure, legend, data and instructions.
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.

In terms of content and format, BioVis papers are expected to:

  • start with a description of the biological context and motivation
  • either introduce novel visualizations or combine existing visualizations in a novel way
  • provide sufficient biological and visualization background
  • end with a discussion where the biological relevance of the visualization methods is discussed

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 2013 Papers". Remember that an abstract is required by April 30, 5 PM PDT for all paper submissions; the full paper and accompanying materials will then have to be submitted by May 7, 5 PM PDT. Authors will be notified about the decision of the Program Committee by July 7.
Papers

Paper Submission Categories

BioVis papers typically fall into one of four categories: technique, system, design study, or evaluation. We briefly discuss these categories below. Although your main paper type has to be specified during the paper submission process, papers can include elements of more than one of these categories.

  • Technique: novel biological visualization techniques or algorithms, or approaches that significantly extend known biological visualization techniques or algorithms. Relevant previous work must be referenced, and the advantage of the new methods over it should be clearly demonstrated. There should be a discussion of the biological tasks and datasets for which this new method is appropriate, and its limitations.
  • System: a blend of visualization algorithms, technical requirements, and design decisions that help biology users deal with the complexity of data management and analysis. The system that is described is both novel and important, and has been implemented. The rationale for significant design decisions is provided, and the system is compared to best-of-breed systems already in use.
  • Application/Design Study: design studies or applications of existing visualization techniques to the biology domain, perhaps within a novel system. Such papers typically explore the choices made when applying visualization to a biology area, for example relating the visual encodings and interaction techniques to the requirements of the target task. The results of the Application / Design Study, including insights generated in the biology domain, should be clearly conveyed.
  • Evaluation: evaluation of the usage of biological visualization by human users, typically through an empirical study of biological visualization techniques or systems, or reports of experience with an existing set of biological visualizations. Authors are not necessarily expected to implement the systems used in these studies themselves; the research contribution will be judged on the validity and importance of the experimental results to biology visualization as opposed to the novelty of the systems or techniques under study.

Please see the Call for Participation for further details about topics of interest.

Regardless of the category, all BioVis papers are expected to start with a description of the biological context and motivation provide sufficient biological and visualization background end with a discussion where the biological relevance of the paper is discussed.

Important Dates

Abstract submission (MANDATORY)
Tuesday, April 30, 2013

Paper submission
Tuesday, May 7, 2013

Notification
Sunday, July 7, 2013

Camera ready copy
Saturday, August 24, 2013

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

Submission 

Please prepare your submission according to the instructions for IEEE Visualization & Graphics Technical Committee (VGTC) conferences. LaTeX and Microsoft Word templates are provided.

BioVis uses the Precision Conference System (PCS) to handle its submission and reviewing process. PCS is available at https://precisionconference.com/~vgtc/. When submitting your manuscript please make sure that you submit it to BioVis by clicking the appropriate header in the conference system landing page.

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

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 VIS website.

Chairs

G. Elisabeta Marai, University of Pittsburgh
Kay Nieselt, University of Tuebingen

Contact: papers@biovis.net

Posters

1. Overview

The BioVis 2013 Posters track offers a venue to present and discuss new research in biological data visualization. Submissions take the form of a short (250-word) abstract with a supporting figure and are presented at the conference site as large format posters during a dedicated poster session. The BioVis symposium as a whole aims to promote interaction between the visualization, bioinformatics, and biology communities, and the BioVis poster session offers an interactive forum that encourages graphical presentation, demonstration, and active engagement with BioVis participants as well as all VisWeek attendees.
 
Important changes from previous years:
  • The submission deadline (August 2, 2013) is now significantly closer to the symposium dates (October 13-14, 2013) to allow for the presentation of late breaking results.
  • We are using a simplified submission process that no longer requires a two-page extended abstract, but instead requires a simple 250-word abstract and a single supporting figure.
  • Given the change in submission format and date, poster abstracts will no longer undergo extensive external review, but rather will be evaluated by the Poster Chairs on an accelerated timeline.
  • Poster abstracts and thumbnail figures will be made public on the BioVis website as in previous years. However, given the much later submission date, authors will not have the opportunity to revise their submitted materials.

2. Submission

Important dates:
Submission Deadline: August 2, 2013
Notification: August 12, 2013
 
Online submission system:
To submit a poster abstract go to https://precisionconference.com/~vgtc, log in, and select  "Submit to Posters" under the BioVis 2013 header on the "new submissions" tab.
 
Requirements:
The following items are required for a complete poster submission:
  • 250-word text-only abstract summarizing the subject matter of the poster. It is critical to clarify the target biological problem, the role of visualization, and the work’s relevance to BioVis.
  • A single figure representative of the work in jpg or png format. It is particularly helpful for this image to illustrate how visualization is being employed to address a biological problem and it will be used as part of the poster submission reviewing process. An accompanying figure legend should be included in the appropriate field of the online submission form.
The large format poster itself is NOT required in the submission. We strongly encourage, but do not require, all authors to include an accompanying video or other supplementary materials according to the VisWeek formatting guidelines http://www.cs.sfu.ca/~vis/Tasks/supplement.html
 
Topics:
Example poster topics include, but are not limited to:
  • Work-in-progress and preliminary results
  • Previously published work from other venues
  • Visualization challenges relevant to the BioVis community
Please see the online BioVis 2013 Call for Participation (CFP) for a full listing of BioVis topics: http://www.biovis.net/year/2013/info/cfp

3. Review Process

Each poster submission will be read and evaluated by the Poster Chairs for quality and relevance to the BioVis venue with the goal of being as inclusive as possible and encouraging cross-domain interactions. Please see the online BioVis 2013 Call for Participation (CFP) for a full listing of BioVis topics: http://www.biovis.net/year/2013/info/cfp. Brief feedback will be provided as needed to support acceptance decisions, but authors should not expect detailed reviews. There will not be a revision cycle. Authors should check their initial abstract submission carefully as this is the copy that will appear on the BioVis web site.

4. Preparing for the Poster Session

At least one author from each accepted submission is required to:  
  1. provide a thumbnail image representing their work 
  2. present a preview of their accepted work in a plenary “fast-forward” session
  3. present an explanatory hardcopy poster during the dedicated poster session
Thumbnail Image:
Accepted posters are asked to provide a thumbnail image that will be used when posting the abstract on the BioVis web site. The image should be a 400x300 pixel jpg or png file. Examples from previous years can be found at http://www.biovis.net/year/2012/posters and http://www.biovis.net/2011/papers_abstracts.html
 
Fast-forward session:
The fast-forward session gives authors the opportunity to promote their poster to the symposium attendees. One author from each poster will have 30 seconds to present one PowerPoint slide summarizing the work. The Poster Chairs will collect and assemble slides from authors in advance of the conference (NOT required for the original submission). 
 
Fast-forward slides should follow these guidelines:
  • PowerPoint compatible (avoid non-standard fonts that might have version compatibility issues)
  • Simple animations are OK, but must be automated (please observe the 30 second time limit)
  • No videos
  • We will include a transition slide with the poster title, number, and author names, so you do not need to include this information
Poster session:
Authors of accepted posters are required to bring an explanatory hardcopy poster for display throughout the BioVis symposium. At least one author should be available at the poster to discuss their work during the scheduled poster session.
 
We strongly encourage authors to show a live demo and/or videos of their work alongside the hardcopy poster. Authors are expected to bring their own equipment for the demo (e.g. laptop), but tables will be provided. We cannot guarantee that power outlets or wireless networking will be available.
The posters themselves have no predefined formatting, but dimensions may not exceed A0 paper size (841mm x 1189mm / 33.1" x 46.8"). Landscape formatting is recommended for compatibility with the presentation boards. The large format poster is only required for the on-site symposium and is NOT part of the original submission.

5. Best Poster Award

A best poster award will be given. Authors of the 'Best Poster' will receive signed certificates during the BioVis Awards session as well as a single joint prize of $250. This award is based on the poster as presented at the poster session. A panel of judges chosen by the Poster Chairs will score their assigned posters and these scores will be used to determine the best poster.

6. Archiving

All abstracts will be considered a "personal communication" to the symposium attendees and will not be published in the proceedings. Abstracts and associated figures will be included with the distributed symposium materials (USB stick) and will appear on the BioVis website. Examples from previous years can be found here:
 

7. Poster Chairs

For details about the symposium or to discuss any aspects of your submission please communicate with the Poster Chairs:
 
 
Robert Kincaid, Agilent Technologies
Cydney Nielsen, British Columbia Cancer Agency, Genome Sciences Centre
 

 

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 VIS website.

Program

  Sunday October 13th
8:30 Welcome & Keynote Session
Scientific Publishing in a Technological Age

Daniel Evanko
10:10 Coffee Break
10:30

Paper Talks 1 - Visualizing Sequence and Omics Data
Chair: Alexander Lex

Primer Talk*: Sequence and Omics Data
Cydney Nielsen

invis: Exploring High-dimensional Sequence Space from In Vitro Selection
Cagatay Demiralp, Eric Hayden, Jeff Hammerbacher, Jeffrey Heer

Large-Scale Multiple Sequence Alignment Visualization through Gradie
Khoa Tan Nguyen, Timo Ropinski

COMBat: Visualizing co-occurrence of annotation terms
Remko van Brakel, Mark Fiers, Christof Francke, Michel Westenberg, Huub van de Wetering

12:00 Lunch Break
14:00

Paper Talks 2 - Visualizing Cellular and Molecular Data
Chair: Jan Aerts

Primer Talk*: Cellular and Molecular Data
Tom Ferrin

Robust Detection and Visualization of Cytoskeletal Structures in Fibrillar Scaffolds from 3-Dimensional Confocal Images
Do Young Park, Desiree Jones, Nicanor I. Moldovan, Raghu Machiraju, Thierry Pecot
 
PresentaBALL - a Powerful Package for Presentations and Lessons in Structural Biology
Stefan Nickels, Daniel Stackel, Sabine C. Mueller, Hans-Peter Lenhof, Andreas Hildebrandt, Anna Katharina Dehof
 
From Biochemical Reaction Networks to 3D Dynamics in the Cell: the ZigCell3D Modeling, Simulation and Visualisation Framework
Pablo de Heras CiechomskiMichael Klann, Robin Mange,  Heinz Koeppl
 
The Molecular Control Toolkit: controlling 3D molecular graphics via gesture and voice
Kenneth Sabir, Christian Stolte, Bruce Tabor, Sean O'Donoghue
 
15:40 Coffee Break
 16:15

Poster Session
Chairs: Cydney Nielsen and Robert Kincaid 

 18:00 BioVis/LDAV Reception
  Monday October 14th
8:30

Paper Talks 3 - Visualizing Networks and Interactions
Chair: Miriah Meyer

Primer Talk*: Networks and Interactions 
Seán O'Donoghue

MoClo Planner: Interactive Visualization for Modular Cloning Bio-Design
Orit Shaer, Consuelo Valdes, Sirui Liu, Kara Lu, Traci Haddock, Swapnil Bhatia, Douglas Densmore, Robert Kincaid
 
VisNEST - Interactive Analysis of Neural Activity Data
Christian Nowke, Maximilian Schmidt, Sacha J, van Albada, Jochen M. Eppler, Rembrandt Bakker, Markus Diesmann, Bernd Hentschel, Torsten Kuhlen
 
neuroMap - Interactive Graph-Visualization of the Fruit Fly's Neural Circuit
Johannes Sorger, Katja Baehler, Florian Schulze, Tianxiao Liu, Barry Dickson
 
Genome-wide detection of sRNA targets with rNAV
Jonathan Dubois, Amine Ghozlane, Patricia Thabault, Isabelle Dutour, Romain Bourqui
 
10:10 Coffee Break
10:30

Paper Talks 4 - Visualizing Population and Function
Chair: Martin Krzywinski

Primer Talk*: Population and Function
Gregory Carter

Leveraging Wall-sized High-Resolution Displays for Comparative Genomics Analyses of Copy Number Variation
Roy Ruddle, Waleed Fateen, Darren Treanor, Peter Sondergeld, Phil Quirke
 
HumMod Browser: An Exploratory Visualization Tool for the Analysis of Whole-Body Physiology Simulation Data
Keqin Wu, Jian Chen, William Pruett, Robert Hester
 
Visual Cleaning of Genotype Data
Jessie Kennedy, Martin Graham, Trevor Paterson, Andy Law
 
12:00 Lunch Break
14:00

Contests Session

Data Contest
Chair: Will Ray 

Fixing TIM: Identifying Functional Mutations in Protein Families through the Interactive Exploration of Sequence and Structural Data
John Wenskovitch, Timothy Luciani, Koonwah Chen, and G. Elisabeta Marai

Visual Analysis of Protein Sequence Mutations with RINalyzer - A BioVis Contest Contribution
Nadezhda T. Doncheva, Karsten Klein, John H. Morris, Francisco S. Domingues, Michael Wybrow, and Mario Albrecht

Mu-8: Visualizing Differences between a Protein and its Family 
John Mercer, Balaji Pandian, Nicolas Bonneel, Alexander Lex, and Hanspeter Pfister

Visualizing Sequence Conservation in Protein Families
Ryo Sakai and Jan Aerts

Seeing the results of a mutation with a vertex-­‐weighted hierarchical graph
Debra Knisley and Jeff Knisley

VERMONT: Visualizing mutations and their effects on protein physicochemical and topological property conservation
Sabrina A. Silveira, Flavia F. Aburjaile, Valdete M. Goncalves-Almeida, Yussif Barcelos, Elisa B. de Lima, Laerte M. Rodrigues, Wagner Meira Jr. and Raquel C. de Melo-Minardi

Introduction to the 2014 Contest - Resting State FMRI
Jason Bohland

Redesign Contest
Chair: Martin Krzywinski

Redesigning the traditional logo plots
Heike Hofmann
 
Sequence Bundles
Marek Kultys
 
Redesign of sequence logos
Ryo Sakai
 
15:40 Coffee Break
16:15

Challenges Session
Chairs: Michel Westenberg and Sean O’Donoghue

Engaging today’s genomics resources
Ting Wang

Tools for Interactive Visualization and Analysis of Complex Biological Structures
Tom Ferrin

17:30 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

Scientific Publishing in a Technological Age

The scientific publishing landscape is changing rapidly and publishers, authors and readers are working hard to adapt. Advances in research technologies are generating increasing amounts of data that require commensurate advances in accessibility, analysis and visualization. Although digital technologies provide possible solutions to allow publishers to fully participate in this revolution and add new capabilities, it has proven challenging to adapt the traditional publishing model to take full advantage of new opportunities. I will discuss these challenges and opportunities and what publishers are doing to meet them from the point of view of a chief editor at Nature Publishing Group. Particular emphasis will be given to data handling and visualization, the role of computer scientists and the challenges in bridging the distinct biology and computer science cultures.
Christof Koch

Daniel Evanko, Ph.D.
Chief Editor, Nature Methods


Daniel Evanko graduated from Northwestern University with a B.S. in Biomedical Engineering. He obtained a Ph.D. in Molecular Pharmacology and Structural Biology and performed post-doctoral work on G protein targeting and regulation at Thomas Jefferson University. As a Research Associate at the University of Pennsylvania Dr. Evanko shifted his scientific focus to fluorescence imaging technologies for studying astrocyte-neuron interactions. He joined the staff of Nature Methods in August of 2004 as an Assistant Editor handling manuscripts and the first issue was published in October. After serving as an Associate and then Senior Editor he became Chief Editor in 2008. While at Nature Methods Dr. Evanko has interviewed dozens of scientists, edited hundreds of manuscripts, written over 100 articles, created and edited a popular column of practical advice on visualizing scientific data, and in 2013 started a new column on statistics. He has been involved in numerous internal initiatives, including ones related to visualization and statistics. 

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.

Engaging today’s genomics resources

Advances in next-generation sequencing platforms have reshaped the landscape of genomic and epigenomic research. Large consortiums such as the ENCyclopedia of DNA Elements (ENCODE), the Roadmap Epigenomics project and The Cancer Genome Atlas (TCGA) have generated tens of thousands of sequencing-based genome-wide datasets, creating a reference and resource for the scientific community. Small groups of researchers are now able to rapidly obtain huge volumes of genomic data and are in great need of putting their own data in the context of the consortium data for comparison. These data are often accompanied by rich metadata describing the sample and experiment, critical for their interpretation. Fast evolving technologies, such as those interrogating long-range chromatin interactions, are generating new types of data in similarly large volumes. Visualizing, navigating, and interpreting such data in a meaningful way is a daunting challenge. In this presentation I will discuss the present challenges in genomic data visualization and the rapid evolution of Genome Browsers.

Inna Dubchak

Ting Wang, Ph.D.
Assistant Professor at the Genetics Department and Center for Genome Sciences, Washington University in St. Louis


Ting Wang is an assistant professor at the Genetics Department and Center for Genome Sciences at Washington University in St. Louis. He has a PhD in Computational Biology. His research focuses on understanding genetic and epigenetic impact of transposable element on human regulatory networks and their role in human diseases. He develops algorithms for identifying regulatory motifs, and analytical and visualization methodologies to integrate genomic and epigenomic data. He is a co-inventor of the UCSC Cancer Genomics Browser, inventor of the Wash U Epigenome Browser, and a co-investigator of the Epigenome Roadmap Mapping Centers.

Tools for Interactive Visualization and Analysis of Complex Biological Structures

As experimental methods to determine the detailed structures of molecules and molecular assemblies continue to rapidly advance, and as databases of modeled macromolecular complexes also swiftly grow in both size and complexity, the challenges of easily visualizing, analyzing, and comparing these structures become increasing difficult.  Particularly onerous are models that encompass scales that range from the atomic to cellular and data that is dynamical in nature.  Yet the ambitious goal of creating an accurate spatiotemporal model of the cell and all of its molecular processes, with maximal accuracy, resolution, and completeness, is nevertheless crucial to a thorough understanding of biological function and the molecular basis of disease.  Because of the complexity of this data, interactive 3D visualization tools greatly facilitate analysis tasks by enabling researchers to explore, interpret, and manipulate their data.  This talk will highlight the challenges associated with visualization of macromolecules at multiple spatial resolutions and illustrate some of the existing tools used to address this problem domain.  Also to be discussed are the challenges that tool builders must face if their tools are to be adopted by the larger scientific community.

Valerie Daggett

Thomas Ferrin, Ph.D.
Professor, Department of Pharmaceutical Chemistry and Department of Bioengineering and Therapeutic Sciences
Director, Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco


Tom originally hails from Minneapolis, where he first became interested in computing while writing codes for a Control Data Corp. model 6600 computer, the first machine to be called a “supercomputer.”  In the early 1970’s, while working as a bioengineer, he became enamored with the application of minicomputers such as the Digital Equipment Corp. PDP-8 and Data General Nova for real-time control and analysis of scientific experiments.  As the data collected from these experiments became larger and more complex, he turned to interactive computer graphics as a means of displaying and analyzing the data, and ultimately gaining insight into the underlying biophysical processes at play.  Thus began a 40+ year career at the University of California, San Francisco (UCSF) focused on developing tools for the interactive visualization and analysis of molecular structure at scales ranging from the atomic to the supramolecular.  In addition to tool development, Tom’s lab has a long history of documenting, distributing, and providing training for these tools.  Their UCSF Chimera package is used worldwide and has been cited in more than 5,400 journal articles.  In recent years his research group has also contributed tools that emphasize integrating diverse types of biomolecular data, including atomic-resolution coordinates, density maps, sequences, annotations, and network representations of protein similarity, binding interactions, and biological pathways.

 

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 2013 - the 3rd 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 2013 will be taking place on 13-14 October 2013 in October 2013 in Atlanta, GA and will be co-located with IEEE VIS 2013. IEEE VIS 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. 

Registration for BioVis 2013 requires registration for IEEE VIS.

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