BioVis@IEEE Challenges Workshop
BioVis@VIS will be held during the main IEEE VIS 2019 program on Thursday October 24th, 2019, over two consecutive sessions: 9:00AM to 10:30 AM and again from 10:50 AM to 12:20 PM. Please see the program, which is now avialable online.
BioVis Challenges Workshop
at IEEE VIS 2019, Vancouver, British Columbia
Aims, Scope & Objectives
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 BioVis Interest Group organizes this interdisciplinary workshop at IEEE VIS, covering aspects of visualization in biology. This workshop 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.
Challenge Formats
Researchers will have two opportunities to participate in this year’s Biovis Challenge. The first is a Data Challenge where researchers are tasked to visualize the tree of life, the second opportunity is a Redesign Challenge where researchers have the opportunity to propose and present a redesign of a biological data visualization of their choosing.
See a summary of our challenges and our expectations here
>Data Challenge
The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. — Charles Darwin
Genomic data is enabling researchers to deeply probe the relatedness of different members of the same species in addition to comparing higher order hierarchical structures between different species. Taken together, genomic data allows us to approximate a tree of life that showcases the relationships of living things. This year’s Biovis challenge will task researchers to visualize this tree of life using data from the RefSeq database. To help researchers with this daunting task, we will be releasing a dataset for analysis and visualization (refer to the background reading for more information).
Submissions to the biovis challenge should be in the form of an open source interactive data visualization, for which we will release additional detailed requirements shortly.
To get updates about the Biovis data challenge, including the dataset release, sign up here: https://forms.gle/aiopkjYChP2PLbQG8
»Dataset
Download the challenge dataset here
The following three files are enclosed within the zip file:
Readme.txt
refseq93.edge.tsv: edge list
refseq93.color
These files contain edges for >= 95% identity matches or RefSeq genomes (release93). Feel free to add additional information that may correspond to the information linked within these files. For example, the taxa id can we used to add additional metadata that are not contained within these existing files.
»Background Reading
Our dataset comes from the following prior publication:
Mash: fast genome and metagenome distance estimation using MinHash. Brian D. Ondov,Todd J. Treangen, Páll Melsted, Adam B. Mallonee, Nicholas H. Bergman, Sergey Koren and Adam M. Phillippy Genome Biology201617:132 doi : https://doi.org/10.1186/s13059-016-0997-x
Figure three in the image (shown below) is an attempt to visualize the data for this challenge. Can you do better?
Although the primary focus of this public is the introduction of a rapidly computable distance metric for genomic data, the focus of this challenge is Figure 3, which visualizes a network of the RefSeq database genomes using the MASH results. Reading this background paper should provide you with an intuition about the dataset and how you might use the properties in this dataset .
»Submission
Submissions can be interactive applications or novel visual encodings. Regardless of what you choose, we encourage participants to share their work publicly. You can submit as many solutions as you like and you can work together in teams. All submissions will be assessed by our panel of experts.
All submissions should be submitted as a poster, conforming to the IEEE VIS poster formatting requirements.
The posters themselves have no predefined formatting, but dimensions may not exceed A0 paper size (841mm x 1189mm / 33.1” x 46.8”). ONLY PORTRAIT FORMAT IS ACCEPTABLE.
Posters are to be submitted as a PDF file with a maximum file size of 10 mb. All poster submissions.
Authors are also encouraged to provide a URL of their submission, which will be assessed at when all submissions are judged in August.
»Important Dates
Submissions Open: June 2019
Submission Closes: August 26th 2019 9PM PDT
Notification of Status: September 10th 2019
>Redesign Challenge
Have you seen a commonly used biomedical data visualization that could be a lot better? Do you have an example of a time you’ve redesigned a data visualization that improved engagement? If so, the redesign challenge is your opportunity to tell that story!
We invited members of the biomedical and data visualization research communities to submit a poster of their redesign process and outcomes. Selected posters will be displayed at the 2019 IEEE VIS conference and the very top posters will be asked to present their work during the Biovis Challenges workshop on Thursday October 24th, 2019.
To receive additional notifications about our biovis redesign challenge please sign up here: https://forms.gle/dM7rqdfwTgq6R72C9
»Submission
All submissions should be submitted as a poster, conforming to the IEEE VIS poster formatting requirements.
The posters themselves have no predefined formatting, but dimensions may not exceed A0 paper size (841mm x 1189mm / 33.1” x 46.8”). ONLY PORTRAIT FORMAT IS ACCEPTABLE.
Posters are to be submitted as a PDF file with a maximum file size of 10 mb. All poster submissions.
»Important Dates
Submissions Open: June 2019
Submission Closes: August 26th 2019 9PM PDT
Notification of Status : September 10 2019
Past BioVis Challenges Workshops
2018 - BioVis Challenges Workshop @ IEEE VIS 2018, Berlin, Germany
2017 - BioVis Challenges Workshop @ IEEE VIS 2017, Phoenix, Arizona, US
Workshop Organizers
Anamaria Crisan, University of British Columbia, Canada (acrisan [at] cs [dot] ubc [dot] ca)
Cydney Nielson, Microsoft, Canada