Visualizing genetic constraints

Principal Components Analysis (PCA) is a common way to study the sources of variation in a high-dimensional data set. Typically, the leading principal components are used to understand the variation in the data or to reduce the dimension of the data for subsequent analysis. The remaining principal components are ignored since they explain little of the variation in the data. However, evolutionary biologists gain important insights from these low variation directions. Specifically, they are interested in directions of low genetic variability that are biologically interpretable. These directions are called genetic constraints and indicate directions in which a trait cannot evolve through selection. Here, we propose studying the subspace spanned by low variance principal components by determining vectors in this subspace that are simplest. Our method and accompanying graphical displays enhance the biologist's ability to visualize the subspace and identify interpretable directions of low genetic variability that align with simple directions.Comment: Published in at http://dx.doi.org/10.1214/12-AOAS603 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

Physics-based visual characterization of molecular interaction forces

Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major aspect where human comprehension and intuition are key to accelerate, analyze, and propose modifications to the molecule of interest. Most visualization algorithms help the users by providing an accurate depiction of the spatial arrangement: the atoms involved in inter-molecular contacts. There are few tools that provide visual information on the forces governing molecular docking. However, these tools, commonly restricted to close interaction between atoms, do not consider whole simulation paths, long-range distances and, importantly, do not provide visual cues for a quick and intuitive comprehension of the energy functions (modeling intermolecular interactions) involved. In this paper, we propose visualizations designed to enable the characterization of interaction forces by taking into account several relevant variables such as molecule-ligand distance and the energy function, which is essential to understand binding affinities. We put emphasis on mapping molecular docking paths obtained from Molecular Dynamics or Monte Carlo simulations, and provide time-dependent visualizations for different energy components and particle resolutions: atoms, groups or residues. The presented visualizations have the potential to support domain experts in a more efficient drug or enzyme design process.Peer ReviewedPostprint (author's final draft

A comparison of two techniques for bibliometric mapping: Multidimensional scaling and VOS

VOS is a new mapping technique that can serve as an alternative to the well-known technique of multidimensional scaling. We present an extensive comparison between the use of multidimensional scaling and the use of VOS for constructing bibliometric maps. In our theoretical analysis, we show the mathematical relation between the two techniques. In our experimental analysis, we use the techniques for constructing maps of authors, journals, and keywords. Two commonly used approaches to bibliometric mapping, both based on multidimensional scaling, turn out to produce maps that suffer from artifacts. Maps constructed using VOS turn out not to have this problem. We conclude that in general maps constructed using VOS provide a more satisfactory representation of a data set than maps constructed using well-known multidimensional scaling approaches

Implementation of a Hybrid Teaching Environment for a Traffic Engineering Course

Students learn in different styles. They learn via hearing and visualizing. They can also reflect and act upon what is presented to them. Afterwards, they start to reason in a logical and intuitive ways as well as memorizing and visualizing, and eventually building mathematical models. Teaching approaches also differ from one course to another and from one instructor to another. Some instructors tend to lecture, others demonstrate or discus while some focus on principles and applications. The quality of student learning process is controlled by the student’s own ability and previous preparation but it also depends on the affinity of the student’s learning style and the instructor’s teaching delivery style. This case study illustrates the transition of a four-thousand level traffic engineering course from a pure face-to-face to a hybrid environment. The implemented hybrid teaching style included one face-to-face weekly lecture besides another lecture being posted online as a YouTube video. Analytical comparisons were conducted between two offerings of the course: before and after the hybrid teaching style Implementation. Based on the presented results, including improved overall grades, student enrollment increase, and positive evaluation feedback, it can be concluded that the implementation process was successful.Cockrell School of Engineerin

Effects of the Electronic Structure, Phase Transition and Localized Dynamics of Atoms in the Formation of Tiny Particles of Gold

In addition to the self-governing properties, tiny metallic colloids are the building blocks of larger particles. This topic has been a subject of many studies. Tiny particles of different sizes developed under three different experiments are discussed in this work. The development of a tiny-sized particle depends on the attained dynamics of atoms. When atoms of the compact monolayer assembly bind by a nanoenergy packet, the developed tiny-sized particle elongates atoms of arrays into the structures of smooth elements at the solution surface. The impinging electron streams at a fixed angle can elongate the already elongated atoms of arrays. Travelling photons along the interface influence the modified atoms. Gold atoms can also develop different tiny particles inside the solution. In addition to the dynamics of atoms, miscellaneous factors can contribute in the development of such tiny particles. Atoms in the form of tiny clusters can also amalgamate to develop a tiny-sized particle. In the third kind of tiny particle, amalgamated atoms can bind by executing electron dynamics. However, not all of the atoms can bind by the electron dynamics. This study very concisely highlights the fundamental process of developing a variety of tiny particles in which electronic structure, phase transition and localized dynamics of gold atoms influence the structure. The study targets the specific discussion that how atoms of tiny-sized particles bind, and how travelling photons along the air-solution interface influence their structure. Several possibilities may be opened through pulse-based process to develop engineered materials

Map Resources – ECO Farms in the Czech Republic

The present paper deals with the creation of maps for the sake of a special map portal using the database of eco farms in the Czech Republic. The map output is being developed and implemented within the framework of the Research Program in mutual cooperation of the Department of Information Technologies, Information and Consulting Centre, other departments of the Faculty of Economics and Management CULS Prague with external partners, especially with the Ministry of Agriculture (Environment and Ecological Agriculture Section, Department of Ecological Agriculture) and the Institute of Agricultural Economics and Information (UZEI) - Division of Agro-environmental Policy in Brno. The maps are visualized by means of MPPR 1.0 system and have been processed – in the pilot stage - for the South Bohemian Region eco farms. The results represent initial data from 2009 (as at 31st December 2009) that have been processed, verified and complemented in the course of 2010

Visualizing practical knowledge: The Haughton-Mars Project

To improve how we envision knowledge, we must improve our ability to see knowledge in everyday life. That is, visualization is concerned not only with displaying facts and theories, but also with finding ways to express and relate tacit understanding. Such knowledge, although often referred to as "common," is not necessarily shared and may be distributed socially in choreographies for working together—in the manner that a chef and a maitre d’hôtel, who obviously possess very different skills, coordinate their work. Furthermore, non-verbal concepts cannot in principle be inventoried. Reifying practical knowledge is not a process of converting the implicit into the explicit, but pointing to what we know, showing its manifestations in our everyday life. To this end, I illustrate the study and reification of practical knowledge by examining the activities of a scientific expedition in the Canadian Arctic—a group of scientists preparing for a mission to Mar