Program BioVis@ISMB

BioVis@ISMB 2016 has now concluded

Check back next year for more opportunities to participate in BioVis@ISMB. We also have a workshop being held in conjunction with IEEE VIS, BioVis@VIS, that will take place in October 2016.

BioVis@ISMB 2016 Program

July 8, 2016

The program features a keynote by Janet Kelso from the Max Planck Institute for Evolutionary Anthropology, a capstone talk about perspectives on data visualization by Dave J Miller from the National Cancer Institute, three sessions with oral presentations selected from submissions to the New Research and Highlight Tracks, as well as a poster session combined with a reception.


The meeting will take place in Pelican 2 (Ground Level - Walt Disney World Swan Hotel, Orlando, FL).

08:30 - 08:45
BioVis Welcome

08:45 - 09:45
Keynote Lecture: Visualization in Ancient Genomics
Janet Kelso University of Leipzig, Germany
Abstract and Speaker Bio

09:45 - 10:20
BioVis Highlights / New Research
09:45 - 10:10

Alistair Ward
IOBIO: interactive, visually-driven, real-time analysis of genomic big data (Highlight)

10:10 - 10:20

Peter Kerpedjiev
Continuous Multi-Scale Exploration of Genome-Wide Interaction Heatmaps (New Research)

10:20 - 10:50
Coffee / Tea Break

10:50 - 12:25
BioVis Highlights / New Research
10:50 - 11:15

Wei Ding
MPAM: an interactive platform for microbial pan-genome analysis and mapping (New Research)

11:15 - 11:25

Sean O’Donoghue
SnapShot: Insulin/IGF1 signaling (Highlight)

11:25 - 11:50

Ricardo Humberto Ramirez Gonzalez
expVIP: a Customizable RNA-Seq Data Analysis and Visualization Platform for non-model organisms (Highlight)

11:50 - 12:15

Aaron Watters & Emily Miraldi
Jupyter Based Visualization and Scripting of Gene Regulatory Network and Genomics Data (New Research)

12:15 - 12:25

W. Jim Zheng
Visualizing Human Genome in Time and Space (New Research)

12:25 - 1:30
Lunch Break
Includes boxed lunch and beverage

01:30 - 01:45
DREAM Visualization Challenge Announcement
01:30 - 01:45

Nils Gehlenborg
DREAM Contest Overview

01:45 - 04:00
BioVis Highlights / New Research
01:45 - 02:10

Kuntal Kumar Bhusan
Web-Igloo: A web based ‘feature decomposition independent’ interactive multivariate data visualization framework (Highlight)

02:10 - 02:35

Sean O’Donoghue
Rondo: interactive visual exploration of chromosome 3D connectivity (New Research)

02:35 - 03:00

Chanin Tolson Woods
Visual exploration of the functional consequence of structure and structure change in RNA ensembles (New Research)

03:00 - 03:25

Alexander Lex
Pathfinder: Visual Analysis of Paths in Graphs (Highlight)

03:25 - 03:35

Will Ray
Myth Unbusted: Evolutionary fingerprints of protein structure do exist in sequences, but you must look in the right place to see them (New Research)

03:35 - 04:00

Garrett Grolemund
Interactive and Reproducible Reporting with R (RStudio Sponsor Tutorial)

04:00 - 04:15
Coffee / Tea Break

04:15 - 05:00
Capstone Talk: NIH Perspectives on Data Visualization
David J Miller National Cancer Institute, Division of Cancer Biology
Abstract and Speaker Bio

05:00 - 05:15
Poster Fast Forward
Will Ray, Michel Westenberg & all poster presenters

05:15 - 05:30
Closing Remarks
Nils Gehlenborg

05:30 - 07:30
Poster Presentation & Reception
Includes beverages and finger food

Keynote Speaker - Janet Kelso

Janet Kelso is a research group leader and Minerva Professor at the Max-Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Her research interests include analysis of ancient genomes, primate comparative genomics and gene expression and the development and application of ontologies for biomedical applications. Her group uses computational approaches to gain insights into genome evolution and has a special interest in the development of novel software for processing and analysis of high-throughput sequence data.

Janet received her PhD in bioinformatics from the South African National Bioinformatics Institute under the supervision of Winston Hide. She is author of more than 70 peer-reviewed scientific publications, co-Editor-in-Chief of the journal Bioinformatics together with Alfonso Valencia, and also an Associate Editor of the journal Database. She is a long-standing and active member of the Board of the International Society for Computational Biology.

Visualisation in Ancient Genomics

The sequencing of the genomes of extinct humans including Neanderthals and Denisovans, as well as the genomes of early modern humans has provided unique insights into the history and demography of human populations. We are now able to study the relationships between archaic groups, to infer population movements and to identify genetic changes that have come to fixation or reached high frequency in modern humans since their divergence from Neandertals and Denisovans. Using Neandertal and Denisovan genome sequences we have shown that gene flow from Neandertals has contributed about 2% of the genomes of present-day non-Africans, while about 4% of the genomes of present-day Oceanians derive from Denisovans. Maps of the Neandertal and Denisovan alleles in present-day non-Africans have allowed us to characterize some of the functional impacts of archaic ancestry on modern humans, while the lengths of these introgressed regions have provided information about the date of admixture. To date, the interpretation of these large and complex ancient DNA datasets has been primarily through statistical analyses. New visualisation methods could contribute to many aspects of the analysis of DNA from ancient organisms. For example, scientists working on ancient DNA would welcome approaches that help them to assess and compare the preservation and contamination present in ancient sequence datasets, or approaches that provide an overview of the genetic relationships between populations over time and across geographical distances. Alignment visualisation methods that allow many thousands of modern and ancient genomes to be compared in order to identify haplotypes that are unique to modern humans, or that are introgressed from archaic humans would also find wide application in the ancient DNA community.

Capstone Speaker - Dave J Miller

David Miller is a program director in the NCI’s Division of Cancer Biology, having joined in 2013 as an AAAS Science & Technology Policy Fellow. A physicist, Dave brings a research background in modeling methods for systems biology and computational toxicology, as well as a broader interest in biomedical software and tools development. In addition to serving within the Physical Sciences-Oncology program, Dave leads the NIH’s Big Data to Knowledge (BD2K) initiative’s Targeted Software Development program, which supports the development of data science software tools, and is active in the NCI’s Informatics Technology for Cancer Research (ITCR) program. Additional program-relevant interests include data visualization, interactive digital media, and crowdsourcing methodologies as applied to biomedical research. Dave completed his Ph.D. in physics at Drexel University (2008), followed by a postdoc at the US Environmental Protection Agency’s National Center for Environmental Assessment (2009-2013). Dave holds a B.A. in physics from the College of Wooster (2002).

NIH Perspectives on Data Visualization