FixingTIM: interactive exploration of sequence and structural data to identify functional mutations in protein families

Visualization of Large Molecular Trajectories

The analysis of protein-ligand interactions is a time-intensive task. Researchers have to analyze multiple physico-chemical properties of the protein at once and combine them to derive conclusions about the protein-ligand interplay. Typically, several charts are inspected, and 3D animations can be played side-by-side to obtain a deeper understanding of the data. With the advances in simulation techniques, larger and larger datasets are available, with up to hundreds of thousands of steps. Unfortunately, such large trajectories are very difficult to investigate with traditional approaches. Therefore, the need for special tools that facilitate inspection of these large trajectories becomes substantial. In this paper, we present a novel system for visual exploration of very large trajectories in an interactive and user-friendly way. Several visualization motifs are automatically derived from the data to give the user the information about interactions between protein and ligand. Our system offers specialized widgets to ease and accelerate data inspection and navigation to interesting parts of the simulation. The system is suitable also for simulations where multiple ligands are involved. We have tested the usefulness of our tool on a set of datasets obtained from protein engineers, and we describe the expert feedback.

Activity-Centered Domain Characterization for Problem-Driven Scientific Visualization

Although visualization design models exist in the literature in the form of higher-level methodological frameworks, these models do not present a clear methodological prescription for the domain characterization step. This work presents a framework and end-to-end model for requirements engineering in problem-driven visualization application design. The framework and model are based on the activity-centered design paradigm, which is an enhancement of human-centered design. The proposed activity-centered approach focuses on user tasks and activities, and allows an explicit link between the requirements engineering process with the abstraction stage-and its evaluation-of existing, higher-level visualization design models. In a departure from existing visualization design models, the resulting model: assigns value to a visualization based on user activities; ranks user tasks before the user data; partitions requirements in activity-related capabilities and nonfunctional characteristics and constraints; and explicitly incorporates the user workflows into the requirements process. A further merit of this model is its explicit integration of functional specifications, a concept this work adapts from the software engineering literature, into the visualization design nested model. A quantitative evaluation using two sets of interdisciplinary projects supports the merits of the activity-centered model. The result is a practical roadmap to the domain characterization step of visualization design for problem-driven data visualization. Following this domain characterization model can help remove a number of pitfalls that have been identified multiple times in the visualization design literature.

Understanding the sequence requirements of protein families: insights from the BioVis 2013 contests

Introduction

In 2011, the BioVis symposium of the IEEE VisWeek conferences inaugurated a new variety of data analysis contest. Aimed at fostering collaborations between computational scientists and biologists, the BioVis contest provided real data from biological domains with emerging visualization needs, in the hope that novel approaches would result in powerful new tools for the community. In 2011 and 2012 the theme of these contests was expression Quantitative Trait Locus analysis, within and across tissues respectively. In 2013 the topic was updated to protein sequence and mutation visualization.

Methods

The contest was framed in the context of a real protein with numerous mutations that had lost function, and the question posed "what minimal set of changes would you propose to rescue function, or how could you support a biologist attempting to answer that question?". The data was grounded in actual experimental results in triosephosphate isomerase(TIM) enzymes. Seven teams composed of 36 individuals submitted entries with proposed solutions and approaches to the challenge. Their contributions ranged from careful analysis of the visualization and analytical requirements for the problem through integration of existing tools for analyzing the context and consequences of protein mutations, to completely new tools addressing the problem.

Results

Judges found valuable and novel contributions in each of the entries, including interesting ways to hierarchicalize the protein into domains of informational interaction, tools for simultaneously understanding both sequential and spatial order, and approaches for conveying some types of inter-residue dependencies. In this manuscript we document the problem presented to the contestants, summarize the biological contributions of their entries, and suggest opportunities that this work has highlighted for even more improved tools in the future.