bbc 2015

BeNeLux Bioinformatics Conference – Antwerp, December 7-8 2015
Abstract ID: P
Poster
10th Benelux Bioinformatics Conference bbc 2015
P3. VISUALIZING BIOLOGICAL DATA THROUGH WEB COMPONENTS
USING POLIMERO AND POLIMERO-BIO
Daniel Alcaide 1,2* , Ryo Sakai 1,2 , Raf Winand 1,2 , Toni Verbeiren 1,2 , Thomas Moerman 1,2 , Jansi Thiyagarajan & Jan Aerts.
KU Leuven Department of Electrical Engineering-ESAT, STADIUS, VDA-lab, Belgium 1 ; iMinds Medical IT, Leuven,
Belgium. * daniel.alcaide@esat.kuleuven.be
Although there are currently several tools for fast prototyping in data visualization, the specifics of the biological domain
often require the development of custom visuals. This leads to the issue that we end up re-implementing the base visuals
over and over if we want to build them into a specific analysis tool. This work presents a proof-of-principle library for
creating composable linked data visualizations, including an initial collection of parsers and visuals with an emphasis on
biology. With Polimero and Polimero-bio, we want to create a library to build scalable domain-specific visual data
exploration tools using a collection of D3-based reusable web components.
INTRODUCTION
As a visual data analysis lab, we often combine
(brush/link) well-known data visualization techniques
(scatterplots, barcharts, etc.). Despite it is possible to use
general-purpose tools like Tableau or Excel, the singular
needs of the biological field usually demand the creation
of particular data visualizations which are not included in
these commercial solutions (Figure 1).
These visuals implementations need to be re-implemented
for each new tool created. The present solution tries to be
an alternative to create composable linked data
visualizations.
Modular: Each element is an independent module
that has a specific purpose (data, visualization,
computation)
Composable: The elements can be combined
setting up new functionalities (linking, filtering,
reading different data sources)
Encapsulated: Web components aim to provide
the user a simple element interface, avoiding to
have to deal with the underlying code.
Reusable: The same element can be used in the
same project for different objectives.
Linkable: Polimero elements can speak to each
other, allowing the use of events for brushing and
linking.
Embeddable: The elements can be added to any
existing frameworks that use HTML (e.g. ipython
notebook).
FIGURE 1. Klaudia-plot - Visualization created with Polimero that shows
the read pairs mapped around a deletion in the NA12878 genome on
chromosome 20.
METHODS
Polimero is a library that uses Polymer implementation for
creating visual web components. (www.polymerproject.org).
Web components are an emerging W3C standard for
extending the HTML platform to create web-based apps.
This new technology includes custom elements, HTML
templates, shadow DOM, and HTML imports (Figure 2).
The D3-based custom elements that Polimero and
Polimero-bio offer, allow us to create a scalable
framework for building domain-specific visual data
exploration tools.
Leveraging the web components concepts, the main
characteristics of Polimero library are:
FIGURE 2. HTML example – Representing Polimero elements to create
visualization.
RESULTS & DISCUSSION
This library makes it possible to create applications that
are composable, encapsulated, and reusable. This is
valuable both for the developer/designer who can easily
create and plug-in custom visual encodings, and for the
end-user who can create linked visualizations by dragging
existing components onto a canvas using the Polimerodesigner.
Polimero and Polimero-bio are still in development but
they are available at www.bitbucket.org/vda-lab/polimero.
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