Standard Visualization Techniques Research Articles

Multidimensional Scaling for Evolutionary Algorithms—Visualization of the Path through Search Space and Solution Space Using Sammon Mapping

Multidimensional scaling as a technique for the presentation of high-dimensional data with standard visualization techniques is presented. The technique used is often known as Sammon mapping. We explain the mathematical foundations of multidimensional scaling and its robust calculation. We also demonstrate the use of this technique in the area of evolutionary algorithms. First, we present the visualization of the path through the search space of the best individuals during an optimization run. We then apply multidimensional scaling to the comparison of multiple runs regarding the variables of individuals and multi-criteria objective values (path through the solution space).

Multidimensional Scaling for Evolutionary Algorithms— Visualization of the Path through Search Space and Solution Space Using Sammon Mapping

Multidimensional scaling as a technique for the presentation of high-dimensional data with standard visualization techniques is presented. The technique used is often known as Sammon mapping. We explain the mathematical foundations of multidimensional scaling and its robust calculation. We also demonstrate the use of this technique in the area of evolutionary algorithms. First, we present the visualization of the path through the search space of the best individuals during an optimization run. We then apply multidimensional scaling to the comparison of multiple runs regarding the variables of individuals and multi-criteria objective values (path through the solution space).

Virtual Tubelets—efficiently visualizing large amounts of particle trajectories

The depiction of particle trajectories is an effective means for the visualization of fluid flows. However, standard visualization techniques suffer from a variety of weaknesses, ranging from ambiguous depth perception for simple line drawings to a high geometrical complexity and decreased interactivity for polygonal tubes. This paper addresses these problems by introducing a novel approach to pathline visualization, which we call Virtual Tubelets. It employs billboarding techniques in combination with suitable textures in order to create the illusion of solid tubes, thus efficiently and unambiguously depicting large amounts of particle trajectories at interactive frame rates. By choosing an appropriate orientation for the billboards, certain issues concerning immersive displays with multiple projection screens are resolved, which allows for an unrestricted use in virtual environments as well. Using modern graphics hardware with programmable vertex and pixel pipelines results in an additional speed-up of the rendering process and a further improvement of image quality. This creates a nearly perfect illusion of tubular geometry, including plausible intersections and consistent illumination with the rest of the scene. The efficiency of our approach is proven by comparing rendering speed and visual quality of Virtual Tubelets to that of conventional, polygonal tube renderings.

Representing protein and peptide structures with parallel-coordinates

Graphical representation of molecular conformations is an important tool used by chemists to gain molecular insight. In spite of today's enhanced computer graphics there are still situations, such as in multiple conformation displays, in which standard visualization techniques are limited. Parallel-coordinate (‖-coords) representation, which was originally developed for visualizing multivariant datasets in fields other than chemistry, offers an alternative basis for graphical representation of molecular structures. In parallel-coordinates, the axes are drawn parallel rather than perpendicular to each other, allowing many axes to be placed and seen. This mapping procedure has unique geometric properties and useful relationships to the original space. In this article, we apply the parallel-coordinate representation for presenting peptide and protein structural conformations. In particular, we demonstrate the usefulness of parallel-coordinates in the context of conformational analysis where this representation, combined with multiple filters, allows nontrivial clustering of data points, leading to new observations. The ‖-coords representation is also demonstrated as a tool for two-dimensional (2D) representation of protein secondary structure and for identification of disulfide-bonded pairs in protein structures. Regardless of the application, an advantage of the ‖-coords approach is that it retains its inherent simplicity and ease of use, and requires little or no software development. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1893–1902, 1997

A Small Flume for Studying the Influence of Hydrodynamic Factors on Benthic Invertebrate Behaviour

A compact, versatile flume for studying the influence of hydrodynamic factors on the behaviour of benthic invertebrates is described. A range of lotic micro-environments can be simulated under controlled and replicable conditions by tailoring the velocity profile at the entrance of the test section. A specially designed diffuser composed of an array of adjustable horizontal rods allows tailored flow (e.g., zone of high shear stress, adjustable velocity gradient and turbulence level) to which organisms can be exposed. Water velocities of up to a maximum of 81.5 ± 0.6 cm/s, with a turbulence intensity of 0.8% can be achieved. Simultaneous observations of flow and organism behaviours can be done by means of standard flow visualization techniques. Compact (72 cm long × 22 cm high × 10 cm wide; volume 10 L) and easily transportable, this flume is an inexpensive "desk-top" version of larger, more bulky systems, without sacrifice of performance and versatility.