2008 - 2010

RNA2DMap

A Google Maps for RNA structures

RNA2DMap - Distance and Conservation

Problem

While working as a research engineer at the Gutell bioinformatics lab at the University of Texas at Austin, I was tasked with the creation of an interactive tool to provide an overview of the lab's insightful but complex work. Armed with two semesters of elective computer science courses and an interest in user interface design, I designed and developed an interactive map for investigating RNA structures.

Roles

Application Developer

I built the interactive visualization application using ActionScript 3.0, Cairngorm MVC framework, XML, PHP, XHTML, CSS, and Subversion. I evolved the application through agile development. 

Interaction Designer

I improved my interactive map experience with navigation, customization, documentation, and linking features.

User Researcher

I conducted usability testing on my application with college students and used the findings to improve the user experience.

Solution

Regions contributing to a folded RNA molecule's structure and function are highly conserved across evolution. RNA2DMap integrated structure, function, and evolutionary data to tell this story interactively.

Explore the RNA structure by panning and zooming. Search for a nucleotide position. Double-click a nucleotide to annotate and save the position.

Explore the RNA structure by panning and zooming. Search for a nucleotide position. Double-click a nucleotide to annotate and save the position.

Hover over a nucleotide to view the physical distance to other nucleotides in the folded RNA molecule; black indicates the closest distance.

Hover over a nucleotide to view the physical distance to other nucleotides in the folded RNA molecule; black indicates the closest distance.

View evolutionary conservation scores for all nucleotides; red indicates the highest level of conservation.

View evolutionary conservation scores for all nucleotides; red indicates the highest level of conservation.

Show data on coaxial stacking, which indicates regions involved in the stability of the folded RNA molecule.

Show data on coaxial stacking, which indicates regions involved in the stability of the folded RNA molecule.

Identify and highlight any significant patterns or motifs present in the RNA sequence and structure.

Identify and highlight any significant patterns or motifs present in the RNA sequence and structure.

Enable, toggle, and customize the display of data sets and the RNA structure.

Enable, toggle, and customize the display of data sets and the RNA structure.

Visualize base pair strengths using a set of symbols invented by the Gutell lab.

Visualize base pair strengths using a set of symbols invented by the Gutell lab.

Access relevant help information in the user guide launched from different contexts in the app.

Access relevant help information in the user guide launched from different contexts in the app.

Download the 3D model of the structure, print the customized view, and open related information from the lab website.

Download the 3D model of the structure, print the customized view, and open related information from the lab website.

Prototyping

I iterated on the design through prototyping, coding, and usability testing.

I learned early on that I only knew enough object-oriented programming to create an unwieldy system. I searched for a better way to structure my application. After discovering the MVC design pattern, I adopted an open-source MVC framework.

RNA2DMap concluded with a publication in the IEEE International Conference on Bioinformatics and Biomedicine.

Poster of RN2DMap

Usability Testing

Between version 1 and version 2 of RNA2DMap, my colleague and I conducted a usability evaluation with 14 participants.

The goal of the study was to evaluate the discovery and effectiveness of RNA2DMap.

I used the results to make improvements to the Comparative RNA Website and the second version of RNA2DMap.

Lessons

Shipping as a motivator – I quickly created something tangible and succeeded in making incremental improvements. Experiencing the benefits of short, iterative cycles early in my career has driven me to replicate a similar cadence of delivery with larger teams and more complex projects.

Design team player – I am motivated more by the output of an iterative process. It made me want to be part of a bigger team working towards better user experiences.