MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Computing in Science and Engineering' source. Sat, 10 Oct 2009 19:30:02 +0100 http://www.medworm.com/index.php?rid=2334467&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814990 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334467 Sat, 18 Apr 2009 04:38:40 +0100 2334467 http://www.medworm.com/index.php?rid=2334466&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814989 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334466 Sat, 18 Apr 2009 04:38:40 +0100 2334466 http://www.medworm.com/index.php?rid=2334465&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814988 Former editor in chief Norman Chonacky waxes lyrical about the trials and tribulations involved in—along with the importance of—learning a new computer language. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334465 Sat, 18 Apr 2009 04:38:40 +0100 2334465 http://www.medworm.com/index.php?rid=2334464&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814987 This issue marks the return of the Computing Prescriptions department; here, the authors describe an algorithm for finding minimum cutsets in connected graphs. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334464 Sat, 18 Apr 2009 04:38:40 +0100 2334464 http://www.medworm.com/index.php?rid=2334463&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814986 The authors have constructed a relatively simple, customized Python module that plugs smoothly into an otherwise standard workflow within VisTrails. This has resulted in the capability to quantitatively analyze complex fluid flows in simulations of merging binary stars. The resulting visualization tool permits researchers to identify values of key rotational frequencies associated with such flows and how these frequencies change over time. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334463 Sat, 18 Apr 2009 04:38:40 +0100 2334463 http://www.medworm.com/index.php?rid=2334462&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814985 In this first installment on postprocessing, we discuss the manner in which the standard grading algorithm can be generalized in order to increase the power and effectiveness of automated grading systems. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334462 Sat, 18 Apr 2009 04:38:40 +0100 2334462 http://www.medworm.com/index.php?rid=2334461&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814984 Parallel programming is bound to become the main concern of software developers in the coming decades. Various models aim to solve this tension, trading efficiency for abstraction or vice versa, but how about getting both? (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334461 Sat, 18 Apr 2009 04:38:40 +0100 2334461 http://www.medworm.com/index.php?rid=2334460&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814983 We can make smaller transistors, but we have a hard time making them run faster. Yet, the demand for computing power is growing. This challenge has led to a renewed interest in novel computing architectures that can take advantage of shrinking transistor size and deliver the necessary application performance improvements. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334460 Sat, 18 Apr 2009 04:38:40 +0100 2334460 http://www.medworm.com/index.php?rid=2334459&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814982 Experimental methods and static quantum calculations can't always give the most realistic picture of the reaction dynamics that laser pulse irradiation induces. Semiclassical dynamics simulations offer an alternative. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334459 Sat, 18 Apr 2009 04:38:40 +0100 2334459 http://www.medworm.com/index.php?rid=2334458&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814981 The authors introduce a new approach to developing Web-enabled environments for remote diagnostics, maintenance, and experimentation in engineering. They've based their approach on a middleware layer, called a Java-Internet-Labview (JIL) server, which provides a transparent mechanism for communicating Java programs with Labview virtual instruments (VIs) running on different computers, without prior communication facilities. Via this layer, the user can control the VI via the Internet, and its controls and indicators become writable and readable from a Java applet. They illustrate their approach by applying it to the development of a complete Web-enabled application for remote control of a thermal process. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334458 Sat, 18 Apr 2009 04:38:40 +0100 2334458 http://www.medworm.com/index.php?rid=2334457&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814980 The parallel coordination of tasks and data is the most significant challenge in high-performance scientific software development. Performance dictates that distributed data communication is best performed outside of a software module, but this comes with a cost of increased coupling and loss of system cohesion. Therefore, developers often face complicated component interactions and distributed data management problems that are hard to design and optimize. The authors developed a software framework called Loci that provides an automatic system for the generating the communication and synchronization that are required to correctly compose software modules. Within Loci, software components only document their needs: the communication coupling between components is removed because the framewo... Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334457 Sat, 18 Apr 2009 04:38:40 +0100 2334457 http://www.medworm.com/index.php?rid=2334456&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814979 Graphics processing units (GPUs) can provide excellent speedups on some, but not all, general-purpose workloads. Using a set of computational GPU kernels as examples, the authors show how to adapt kernels to utilize the architectural features of a GeForce 8800 GPU and what finally limits the achievable performance. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334456 Sat, 18 Apr 2009 04:38:40 +0100 2334456 http://www.medworm.com/index.php?rid=2334455&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814978 Partial differential equations (PDEs) are ubiquitous to the mathematical description of physical phenomena. Typical examples describe the evolution of a field in time as a function of its value in space, such as in wave propagation or heat flow. Many existing PDE solver packages focus on the important, but arcane, task of actually numerically solving the linearized set of algebraic equations that result from the discretization of a set of PDEs, but the need for many researchers is often higher level than that. They have the physical knowledge to describe their model, and can apply differential calculus to obtain appropriate governing conditions, but when faced with rendering those governing equations on a computer, their skills (or time) are limited to explicit finite differences on unifor... Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334455 Sat, 18 Apr 2009 04:38:40 +0100 2334455 http://www.medworm.com/index.php?rid=2334454&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814977 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334454 Sat, 18 Apr 2009 04:38:40 +0100 2334454 http://www.medworm.com/index.php?rid=2334453&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814976 Associate editor in chief Douglass Post describes the importance of simulation for engineering design resources. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334453 Sat, 18 Apr 2009 04:38:40 +0100 2334453 http://www.medworm.com/index.php?rid=2334452&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814975 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334452 Sat, 18 Apr 2009 04:38:40 +0100 2334452 http://www.medworm.com/index.php?rid=2334451&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814974 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334451 Sat, 18 Apr 2009 04:38:40 +0100 2334451 http://www.medworm.com/index.php?rid=2334450&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4814972%26arnumber%3D4814973 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2334450 Sat, 18 Apr 2009 04:38:40 +0100 2334450 http://www.medworm.com/index.php?rid=2310033&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784389 Michael J. Schillaci reviews Advances in Discrete Tomography and Its Applications. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2310033 Wed, 08 Apr 2009 07:35:07 +0100 2310033 http://www.medworm.com/index.php?rid=2251937&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784405 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251937 Wed, 11 Mar 2009 14:51:41 +0100 2251937 http://www.medworm.com/index.php?rid=2251936&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784404 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251936 Wed, 11 Mar 2009 14:51:41 +0100 2251936 http://www.medworm.com/index.php?rid=2251935&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784403 Columnist Charles Day describes the history of computing as presented in the James Bond movie series. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251935 Wed, 11 Mar 2009 14:51:41 +0100 2251935 http://www.medworm.com/index.php?rid=2251934&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784402 Most computational codes that use irregular grids depend on the single worst triangle's quality: skinny triangles can lead to bad performance and numerical instabilities. Marching cubes (MC) is the standard isosurface grid generation algorithm, and, whereas most triangles it generates are good, it almost always generates some bad triangles. Here, we show how simple changes to MC can lead to a drastically reduced number of degenerate triangles, making it a more practical choice for isosurface grid generation, reducing or eliminating the need for and cost of postprocessing. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251934 Wed, 11 Mar 2009 14:51:41 +0100 2251934 http://www.medworm.com/index.php?rid=2251933&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784401 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251933 Wed, 11 Mar 2009 14:51:41 +0100 2251933 http://www.medworm.com/index.php?rid=2251932&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784400 The curvelet transform allows an almost optimal nonadaptive sparse representation for curve-like features and edges. The authors describe some recent applications involving image processing, seismic data exploration, turbulent flows, and compressed sensing. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251932 Wed, 11 Mar 2009 14:51:41 +0100 2251932 http://www.medworm.com/index.php?rid=2251931&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784399 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251931 Wed, 11 Mar 2009 14:51:41 +0100 2251931 http://www.medworm.com/index.php?rid=2251930&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784398 In this article, the authors explore various uses of inexpensive embedded Linux devices such as the Linksys NSLU2 ("slug"). Embedded computing is a topic of growing interest. Although novel architectures such as cell processors, graphics processors (GPUs), and FPGAs are growing in popularity, conventional microproessor designs such as Intel's Xscale (ARM) and Atom pack a punch in a small footprint, not to mention being widely supported by commodity operating system and development tools. We're convinced that this entire space is a tool worth keeping in the scientific programmer's and software developer's toolchests. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251930 Wed, 11 Mar 2009 14:51:41 +0100 2251930 http://www.medworm.com/index.php?rid=2251929&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784397 Adobe Illustrator CS3 provides sufficient tools that let chemistry textbook and laboratory manual authors create complex drawings and publish their own original material. In this final tutorial, the author describes how to fine tune an illustration. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251929 Wed, 11 Mar 2009 14:51:41 +0100 2251929 http://www.medworm.com/index.php?rid=2251928&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784396 Direct numerical simulation (DNS) of turbulence is computationally intensive and typically relies on some form of parallel processing. Spectral kernels used for spatial discretization are a common computational bottleneck on distributed memory architectures. One way to increase DNS algorithms' efficiency is to parallelize spectral kernels using tightly coupled single-program, multiple-data (SPMD) multiprocessor units with minimal interprocessor communication latency. The authors present techniques to map DNS computations to modern graphics processing units (GPUs), which are characterized by very high memory bandwidth and hundreds of SPMD processors. The article compares the performance between the authors' parallel algorithm running on a GPU versus the associated CPU implementation of a so... Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251928 Wed, 11 Mar 2009 14:51:41 +0100 2251928 http://www.medworm.com/index.php?rid=2251927&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784395 The advent of affordable parallel computers such as Beowulf PC clusters and, more recently, multicore PCs has been highly beneficial for a large number of scientists and smaller institutions that might not otherwise have access to substantial computing facilities. However, there hasn't been an analogous progress in the development and dissemination of parallel software—scientists need the expertise to develop parallel codes and must invest a significant amount of time in the development of tools even for the most common data-analysis tasks. The authors describe the Beowulf Analysis Symbolic INterface (BASIN), a multiuser parallel data analysis and visualization framework. BASIN is aimed at providing scientists with a suite of parallel libraries for astrophysical data analysis along... Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251927 Wed, 11 Mar 2009 14:51:41 +0100 2251927 http://www.medworm.com/index.php?rid=2251926&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784394 The fields of radiation and hydrodynamics are time-honored disciplines in physics. However, it's only since the nuclear age that the importance of radiation hydrodynamics—a single field studying the interplay of radiation and material hydrodynamics together—has come into prominence. Similarly, it's only since the computer age that physically interesting problems in this field have become tractable. In this article, the authors discuss the process of building a model to study one of the fundamental problems of astrophysics: the supernova explosion of a massive star caused by the collapse of its core. An explanation for the mechanism of this explosion involves the interaction of material hydrodynamics and neutrino radiation. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251926 Wed, 11 Mar 2009 14:51:41 +0100 2251926 http://www.medworm.com/index.php?rid=2251924&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784393 A common feature of astrophysical flows is that they typically span a broad range of length and time scales. Specialized numerical algorithms that exploit the relationships between these scales can significantly improve the efficiency of numerical simulations without loss of accuracy. In the case of highly subsonic flows, hydrodynamics algorithms that filter sound waves but retain both local and large-scale compressibility effects can give accurate and efficient solutions. The authors describe the process by which an understanding of the important processes in Type Ia supernovae is guiding the development of new algorithms to model these phenomena. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251924 Wed, 11 Mar 2009 14:51:41 +0100 2251924 http://www.medworm.com/index.php?rid=2251922&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784392 Due to the small width of the subsonic burning front (flame) in thermonuclear supernovae, micrometers to centimeters, and the influence of turbulence, which adds structure to this front on a broad range of scales, it won't be possible in the foreseeable future to resolve the burning front in full-star simulations with typical scales of thousands of kilometers. This problem is far from unique to astrophysics. In many hydrodynamic studies in the laboratory, including pre-mixed combustion, the viscous scale, at which turbulence is dissipated, and the reaction front can't be resolved in simulations of realistic applications. Under these circumstances, so-called large eddy simulations (LES) are used, which employ models in place of unresolved physics. The adaptation and usage of models for unre... Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251922 Wed, 11 Mar 2009 14:51:41 +0100 2251922 http://www.medworm.com/index.php?rid=2251921&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784391 This special astrophysics issue presents three case studies on modeling supernovae, which are spectacular stellar explosions. A fourth paper presents a set of parallel analytical tools being developed to analyze the complex results of such simulations. Many astrophysics problems include multiple interacting physical processes and involve disparate length and time scales. Such multiphysics, multiscale applications are challenging to model and require the largest extant computers to simulate. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251921 Wed, 11 Mar 2009 14:51:41 +0100 2251921 http://www.medworm.com/index.php?rid=2251920&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784390 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251920 Wed, 11 Mar 2009 14:51:41 +0100 2251920 http://www.medworm.com/index.php?rid=2251919&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784389 Michael J. Schillaci reviews Advances in Discrete Tomography and Its Applications. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251919 Wed, 11 Mar 2009 14:51:41 +0100 2251919 http://www.medworm.com/index.php?rid=2251918&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784388 In recognition of the general lack of exposure scientists have to software engineering and vice versa, a workshop was held during the 2008 International Conference on Software Engineering in Leipzig, Germany. The workshop's goal was to bring together researchers and practitioners from the software engineering and computational science and engineering (CS&E) communities to build a common understanding of the issues involved in the complex process of CS&E software development and identify common themes to pursue in future research. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251918 Wed, 11 Mar 2009 14:51:41 +0100 2251918 http://www.medworm.com/index.php?rid=2251917&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784387 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251917 Wed, 11 Mar 2009 14:51:41 +0100 2251917 http://www.medworm.com/index.php?rid=2251916&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784386 Computing in Science & Engineering delivers high-quality peer-reviewed articles only through the efforts of our volunteers. Although individual reviews are performed confidentially, we would like to take the opportunity to publicly thank our 2008 reviewers for their gracious efforts. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251916 Wed, 11 Mar 2009 14:51:41 +0100 2251916 http://www.medworm.com/index.php?rid=2251915&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784385 Editor-in-chief Isabel Beichl describes how computational scientists and engineers can help improve their current IT situations. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251915 Wed, 11 Mar 2009 14:51:41 +0100 2251915 http://www.medworm.com/index.php?rid=2251914&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784384 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251914 Wed, 11 Mar 2009 14:51:41 +0100 2251914 http://www.medworm.com/index.php?rid=2251913&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784383 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251913 Wed, 11 Mar 2009 14:51:41 +0100 2251913 http://www.medworm.com/index.php?rid=2251911&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4784381%26arnumber%3D4784382 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2251911 Wed, 11 Mar 2009 14:51:41 +0100 2251911 http://www.medworm.com/index.php?rid=2078410&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720230 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078410 Sun, 04 Jan 2009 14:18:33 +0100 2078410 http://www.medworm.com/index.php?rid=2078409&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720229 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078409 Sun, 04 Jan 2009 14:18:33 +0100 2078409 http://www.medworm.com/index.php?rid=2078408&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720228 Contributing editor Francis Sullivan ponders the difference between experiencing evolutionary shocks in real life versus computational life. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078408 Sun, 04 Jan 2009 14:18:33 +0100 2078408 http://www.medworm.com/index.php?rid=2078407&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720227 pMatlab, a parallel Matlab library, lowers the barrier to development of parallel and distributed application codes by providing an easy-to-use programming environment. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078407 Sun, 04 Jan 2009 14:18:33 +0100 2078407 http://www.medworm.com/index.php?rid=2078406&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720226 Granular materials: what are they, and how can we generate them on computers? How do we characterize such systems both quantitatively and qualitatively? How does a granular pile respond to an external force? How can we access and interpret the internal structure of granular materials at micro- and macroscales? This installment of Computer Simulations approaches these questions by reviewing a range of granular material theories and numerical simulation techniques. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078406 Sun, 04 Jan 2009 14:18:33 +0100 2078406 http://www.medworm.com/index.php?rid=2078405&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720225 Creating an interactive digital holographic display is a challenging task, requiring input from mathematics, physics and engineering. The main technological hurdle to develop holographic displays is sheer computational speed. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078405 Sun, 04 Jan 2009 14:18:33 +0100 2078405 http://www.medworm.com/index.php?rid=2078404&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720224 Adobe Illustrator CS3 provides tools that let authors of chemistry textbooks and laboratory manuals create complex drawings and publish their own original material. Part 2 of this three-part tutorial focuses on shapes. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078404 Sun, 04 Jan 2009 14:18:33 +0100 2078404 http://www.medworm.com/index.php?rid=2078403&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720223 Janus is a modular, massively parallel, and reconfigurable FPGA-based computing system. Each Janus module has one computational core and one host. Janus is tailored to, but not limited to, the needs of a class of hard scientific applications characterized by regular code structure, unconventional data-manipulation requirements, and a few Megabits database. The authors discuss this configurable system's architecture and focus on its use for Monte Carlo simulations of statistical mechanics, as Janus performs impressively on this class of application. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078403 Sun, 04 Jan 2009 14:18:33 +0100 2078403 http://www.medworm.com/index.php?rid=2078402&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720222 Rappture is a new GUI development kit that enables a developer to build an I/O interface for a specific application. In this article, the authors describe the Rappture toolkit's use in generating a GUI for the Zori computer code, a quantum Monte Carlo program. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078402 Sun, 04 Jan 2009 14:18:33 +0100 2078402 http://www.medworm.com/index.php?rid=2078401&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720221 As computational researchers increasingly make their results available in a reproducible way, and often outside the traditional journal publishing mechanism, questions naturally arise with regard to copyright, subsequent use and citation, and ownership rights in general. The growing number of scientists who release their research publicly face a gap in the current licensing and copyright structure, particularly on the Internet. Scientific research produces more than the final paper: The code, data structures, experimental design and parameters, documentation, and figures are all important for scholarship communication and result replication. The author proposes the reproducible research standard for scientific researchers to use for all components of their scholarship that should encourage... Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078401 Sun, 04 Jan 2009 14:18:33 +0100 2078401 http://www.medworm.com/index.php?rid=2078400&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720220 The ability to make scientific findings reproducible is increasingly important in areas where substantive results are the product of complex statistical computations. Reproducibility can allow others to verify the published findings and conduct alternate analyses of the same data. A question that arises naturally is how to conduct and distribute reproducible research. The authors describe a simple framework in which reproducible research can be conducted and distributed via cached computations and tools for both authors and readers. As a prototype implementation they also describe a software package written in the R language. The "cacher" package provides tools for caching computational results in a key-value style database, which can be published to a public repository for readers to down... Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078400 Sun, 04 Jan 2009 14:18:33 +0100 2078400 http://www.medworm.com/index.php?rid=2078399&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720219 Reproducible research in computational science is only possible if the computer codes used to generate published results are distributed and/or archived in a form that can later be used to regenerate the results and can be examined to determine details of the method used. The author discusses some difficulties in achieving this goal and surveys a set of Python tools for facilitating reproducible research on finite volume methods for hyperbolic conservation laws using the Clawpack software. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078399 Sun, 04 Jan 2009 14:18:33 +0100 2078399 http://www.medworm.com/index.php?rid=2078398&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720218 Scientific computation is emerging as absolutely central to the scientific method. Unfortunately, it's error-prone and currently immature—traditional scientific publication is incapable of finding and rooting out errors in scientific computation—which must be recognized as a crisis. An important recent development and a necessary response to the crisis is reproducible computational research in which researchers publish the article along with the full computational environment that produces the results. The authors have practiced reproducible computational research for 15 years and have integrated it with their scientific research and with doctoral and postdoctoral education. In this article, they review their approach and how it has evolved over time, discussing the argumen... Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078398 Sun, 04 Jan 2009 14:18:33 +0100 2078398 http://www.medworm.com/index.php?rid=2078397&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720217 Reproducibility is a core principle of science. For computational experiments to become reproducible, one needs to develop a system for linking scientific publications with computational recipes. Articles in this special issue argue in favor of computational reproducibility and describe several practical approaches to reproducible research. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078397 Sun, 04 Jan 2009 14:18:33 +0100 2078397 http://www.medworm.com/index.php?rid=2078396&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720216 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078396 Sun, 04 Jan 2009 14:18:33 +0100 2078396 http://www.medworm.com/index.php?rid=2078395&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720215 CiSE was created to serve the computational science community. From its founding, it has focused on real-world applications of scientific computing, with articles written by and for active practitioners, and it will continue to serve this function. Education in computational science is a core mission for CiSE. Its feature articles are designed to inform and instruct, and various columns appearing in every issue are explicitly tutorial. CiSE has always been a group effort, with a editorial board of industry activists. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078395 Sun, 04 Jan 2009 14:18:33 +0100 2078395 http://www.medworm.com/index.php?rid=2078394&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720214 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078394 Sun, 04 Jan 2009 14:18:33 +0100 2078394 http://www.medworm.com/index.php?rid=2078393&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720213 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078393 Sun, 04 Jan 2009 14:18:33 +0100 2078393 http://www.medworm.com/index.php?rid=2078392&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4720211%26arnumber%3D4720212 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2078392 Sun, 04 Jan 2009 14:18:33 +0100 2078392 http://www.medworm.com/index.php?rid=1906600&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653217 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906600 Sat, 25 Oct 2008 14:27:40 +0100 1906600 http://www.medworm.com/index.php?rid=1906599&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653216 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906599 Sat, 25 Oct 2008 14:27:40 +0100 1906599 http://www.medworm.com/index.php?rid=1906598&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653215 Contributor Charles Day ponders the extent to which software enhances hardware and the other devices we've come to rely on daily. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906598 Sat, 25 Oct 2008 14:27:40 +0100 1906598 http://www.medworm.com/index.php?rid=1906597&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653214 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906597 Sat, 25 Oct 2008 14:27:40 +0100 1906597 http://www.medworm.com/index.php?rid=1906596&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653213 Adobe Illustrator CS3 provides sufficient tools to let authors of chemistry textbooks and laboratory manuals create complex drawings and publish their own original materials. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906596 Sat, 25 Oct 2008 14:27:40 +0100 1906596 http://www.medworm.com/index.php?rid=1906595&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653212 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906595 Sat, 25 Oct 2008 14:27:40 +0100 1906595 http://www.medworm.com/index.php?rid=1906594&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653211 Sheets stacked within layers are common in clay; coarse-grained computer simulation modeling can predict how to disperse the layers in a different solvent matrix. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906594 Sat, 25 Oct 2008 14:27:40 +0100 1906594 http://www.medworm.com/index.php?rid=1906593&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653210 Transfer functions play a critical role in feature detection through direct volume rendering in volumetric scalar fields. Because of the inherent difficulties of exploratory visualization, assisting the user in transfer-function specification is still an important research area. In particular, the disparate nature of simulated and measured unstructured volumetric data necessitates more flexibility in the specification process than existing tools provide. Here, the authors introduce a framework that combines elements of existing techniques and introduces new features to handle the diversity of volumetric data sets. The authors discuss a range-mapping technique for assisting in transfer-function specification for high-dynamic range data, an algorithm for combining multiple transfer functions... Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906593 Sat, 25 Oct 2008 14:27:40 +0100 1906593 http://www.medworm.com/index.php?rid=1906592&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653209 The department editors discuss the continuing importance of requirements, managing Web content, free public Wi-Fi, and a recent personal transition to Internet telephony. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906592 Sat, 25 Oct 2008 14:27:40 +0100 1906592 http://www.medworm.com/index.php?rid=1906591&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653208 Recently developed by William Stein of the University of Washington, Sage is a free, open source mathematical software system written in Python with impressive capabilities. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906591 Sat, 25 Oct 2008 14:27:40 +0100 1906591 http://www.medworm.com/index.php?rid=1906590&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653207 The SDSS is one of the first very large archives in astronomy and other sciences, as we enter the era of data-intensive science. Here the authors summarize some of the important and generally applicable insights they have gained (often the hard way!) over the past decade of SDSS development. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906590 Sat, 25 Oct 2008 14:27:40 +0100 1906590 http://www.medworm.com/index.php?rid=1906589&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653206 The UK Met Office's Flexible Configuration Management (FCM) system uses existing open source tools, adapted for use with high-performance scientific Fortran code, to help manage evolving code in its large-scale climate simulation and weather forecasting models. FCM has simplified the development process, improved team coordination, and reduced release cycles. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906589 Sat, 25 Oct 2008 14:27:40 +0100 1906589 http://www.medworm.com/index.php?rid=1906588&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653205 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906588 Sat, 25 Oct 2008 14:27:40 +0100 1906588 http://www.medworm.com/index.php?rid=1906587&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653204 The Quantum Chromodynamics Parallel Computing on the Cell Broadband Engine (QPACE) project is developing a massively parallel, scalable supercomputer for applications in lattice quantum chromodynamics (QCD). Specifically, the architecture is a 3D torus of identical processing nodes, based on the PowerXCell 8i processor. These nodes are tightly coupled by an application-optimized network processor that is based on a field-programmable gate array attached to the PowerXCell 8i. The authors have analyzed lattice QCD code performance on QPACE, carried out corresponding hardware benchmarks, and found that it offers suitable performance. They describe the QPACE architecture in detail, focusing on the challenges arising from the PowerXCell 8i's multicore nature and the use of an FPGA for the netwo... Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906587 Sat, 25 Oct 2008 14:27:40 +0100 1906587 http://www.medworm.com/index.php?rid=1906586&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653203 Field-programmable gate arrays are widely considered accelerators for compute-intensive applications. A critical phase of FPGA application development is finding and mapping to the appropriate computing model. These models differ from models generally used in programming. For example, whereas parallel computing models are often based on thread execution and interaction, FPGA computing can exploit more degrees of freedom than are available in software. This enables models with highly flexible fine-grained parallelism and associative operations such as broadcast and collective response. Several case studies demonstrate the effectiveness of using FPGA-based accelerators in molecular modeling. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906586 Sat, 25 Oct 2008 14:27:40 +0100 1906586 http://www.medworm.com/index.php?rid=1906585&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653202 Graphical processing units (GPUs) are rapidly outpacing conventional CPUs in computational performance. The authors provide a brief overview of electronic structure theory and detail their experiences implementing quantum chemistry methods on the GPU, demonstrating speedups of up to 93x for direct self-consistent field calculations on a variety of molecules. They analyze the performance of the algorithms in terms of floating-point operations and memory bandwidth. They also assess the adequacy of the single-precision accuracy for quantum chemistry applications. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906585 Sat, 25 Oct 2008 14:27:40 +0100 1906585 http://www.medworm.com/index.php?rid=1906584&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653201 A restructuring method for implementing numerical algorithms for scientific computing can help them run efficiently on the IBM Cell processor and other multicore CPUs. Using the PPM gas dynamics algorithm as an example, this work walks through code transformation techniques step by step that can boost performance of scientific simulation codes. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906584 Sat, 25 Oct 2008 14:27:40 +0100 1906584 http://www.medworm.com/index.php?rid=1906583&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653200 As chip designers struggle to increase the speed of conventional microprocessors, the scientific computing community is turning its attention to alternative architectures that utilize computational accelerators to improve the application performance. This special issue of CiSE examines several examples of computationally demanding applications implemented on novel high-performance computing architectures and points out the challenges and opportunities that these new architectures bring up. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906583 Sat, 25 Oct 2008 14:27:40 +0100 1906583 http://www.medworm.com/index.php?rid=1906582&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653199 Timothy P. Chartier reviews Google's PageRank and Beyond: The Science of Search Engine Rankings by Amy Langville and Carl Meyer. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906582 Sat, 25 Oct 2008 14:27:40 +0100 1906582 http://www.medworm.com/index.php?rid=1906581&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653198 Graphic processing units (GPU) provide an impressive amount of computer power at an unprecedented low cost. The authors describe the main features of HOOMD (highly optimized object oriented molecular dynamics), a software package that makes molecular dynamics simulations on GPUs available to general users. Also, a news sidebar by Joshua A. Anderson and Alex Travesset on Molecular Dynamics on Graphic Processing Units: HOOMD to the Rescue. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906581 Sat, 25 Oct 2008 14:27:40 +0100 1906581 http://www.medworm.com/index.php?rid=1906580&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653197 Editor-in-chief Norman Chonacky's swan song describes the past four years of his tenure helming the magazine and welcomes in the new editor in chief, Isabel Beichl. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906580 Sat, 25 Oct 2008 14:27:40 +0100 1906580 http://www.medworm.com/index.php?rid=1906579&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653196 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906579 Sat, 25 Oct 2008 14:27:40 +0100 1906579 http://www.medworm.com/index.php?rid=1906578&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653195 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906578 Sat, 25 Oct 2008 14:27:40 +0100 1906578 http://www.medworm.com/index.php?rid=1906577&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4653193%26arnumber%3D4653194 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1906577 Sat, 25 Oct 2008 14:27:40 +0100 1906577 http://www.medworm.com/index.php?rid=1603520&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548213 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603520 Thu, 10 Jul 2008 17:18:01 +0100 1603520 http://www.medworm.com/index.php?rid=1603519&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548212 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603519 Thu, 10 Jul 2008 17:18:01 +0100 1603519 http://www.medworm.com/index.php?rid=1603518&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548211 Starting from first principles, physicists intrepidly tackle such problems as the origin of life or human consciousness. In that same spirit of boldness, Charles Day attempts to gauge the Web's future impact on scientific journals. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603518 Thu, 10 Jul 2008 17:18:01 +0100 1603518 http://www.medworm.com/index.php?rid=1603517&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548210 Columnist Paul F. Dubois says good-bye to his readers in this, his final installment of Café Dubois. This entertaining history of how the column came to be follows his own career path/arc. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603517 Thu, 10 Jul 2008 17:18:01 +0100 1603517 http://www.medworm.com/index.php?rid=1603516&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548209 When building large scientific codes, you might have to mix different programming languages. The authors show how to bridge the interoperability gap between Fortran 90/95 and C, and from C to other languages, with working code examples. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603516 Thu, 10 Jul 2008 17:18:01 +0100 1603516 http://www.medworm.com/index.php?rid=1603515&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548208 Are high-resolution digital holographic displays just around the corner? In the 1990s, two hurdles seemed to be preventing the practical implementation of computational holography techniques: computational workload and hardware projection capabilities. Are these hurdles still in place? (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603515 Thu, 10 Jul 2008 17:18:01 +0100 1603515 http://www.medworm.com/index.php?rid=1603514&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548207 In the second part of a two-part series, the authors discuss massively parallel strategies for numerically solving wave propagation in heterogeneous media. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603514 Thu, 10 Jul 2008 17:18:01 +0100 1603514 http://www.medworm.com/index.php?rid=1603513&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548206 This three-part series shows how applying knowledge about the underlying computer hardware to the code for a simple but computationally intensive algorithm can significantly improve performance. This second segment focuses on memory accesses. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603513 Thu, 10 Jul 2008 17:18:01 +0100 1603513 http://www.medworm.com/index.php?rid=1603512&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548205 The authors discuss the important questions that benchmarking must answer and the degree to which such answers can be given by existing kernel versus real application benchmarks. They describe the state of the art and challenges that must be met to base needed performance measurements on real applications. Finally, they quantify their claims by measuring and comparing several real applications and kernel benchmarks. An important finding is that all three measured computer platforms performed both the best and the worst across the selected applications; "best performance" significantly depended on the problem being solved, questioning the value of computer rankings that use simplistic metrics. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603512 Thu, 10 Jul 2008 17:18:01 +0100 1603512 http://www.medworm.com/index.php?rid=1603511&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548204 This article shows examples of laboratory assignments that the authors' students must complete for a course on system identification and control. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603511 Thu, 10 Jul 2008 17:18:01 +0100 1603511 http://www.medworm.com/index.php?rid=1603510&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548203 The program tool Thermath now lets researchers automatically generate complete, ready-to-use Matlab functions. The examples here deal with critical-point calculations and the development of equipment models for separations in the chemical industry, but the ability to automatically generate Matlab functions is useful in many areas of science and engineering. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603510 Thu, 10 Jul 2008 17:18:01 +0100 1603510 http://www.medworm.com/index.php?rid=1603509&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548202 The semi-implicit integration scheme is often used to simulate cloth animation because of its high stability and efficiency. However, it gives notable vibrations because of linear approximation in large rotations, which always occur in cloth simulations. Hence, most simulations are inaccurate and inefficient, with the number of iterations increasing enormously and vibrating significantly in adjacent time steps. In this article, the authors propose a novel physical model that is both stable and efficient when simulating cloth with large rotations. Furthermore, their approach introduces fewer artificial damping effects than in previously proposed semi-implicit methods. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603509 Thu, 10 Jul 2008 17:18:01 +0100 1603509 http://www.medworm.com/index.php?rid=1603508&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548201 The authors describe a data exploration system that visualizes time-varying, multivariate, point-based data from gyrokinetic particle simulations. By using two interaction modes, their system lets researchers explore collections of densely packed particles and discover interesting aspects, such as the location and motion of particles trapped in turbulent plasma flow. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603508 Thu, 10 Jul 2008 17:18:01 +0100 1603508 http://www.medworm.com/index.php?rid=1603507&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548200 A new multiscale approach for simulating nanobiological flows uses concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The approach is based on a simple scheme of space–time information exchange between the atomistic and mesoscopic scales. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603507 Thu, 10 Jul 2008 17:18:01 +0100 1603507 http://www.medworm.com/index.php?rid=1603506&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548199 The Astronomical Medicine Project (http://astromed.iic.harvard.edu/) is working to convert medical imaging software into tools that fuel discoveries in astronomy. But if the scientists behind the project have their way, any discipline that relies on large, complex data sets will reap the benefits. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603506 Thu, 10 Jul 2008 17:18:01 +0100 1603506 http://www.medworm.com/index.php?rid=1603505&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548198 The articles in this issue cover mechanics, biology, and laboratory applications, and three cover computation per se. Moreover, they're evenly divided between the two categories of CiSE readers. CiSE thus seems to be fulfilling its mission of establishing a liaison between the physical sciences and computational sciences. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603505 Thu, 10 Jul 2008 17:18:01 +0100 1603505 http://www.medworm.com/index.php?rid=1603504&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548197 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603504 Thu, 10 Jul 2008 17:18:01 +0100 1603504 http://www.medworm.com/index.php?rid=1603503&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548196 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603503 Thu, 10 Jul 2008 17:18:01 +0100 1603503 http://www.medworm.com/index.php?rid=1603502&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4548194%26arnumber%3D4548195 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1603502 Thu, 10 Jul 2008 17:18:01 +0100 1603502 http://www.medworm.com/index.php?rid=1561828&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418778.pdf%3Fisnumber%3D4418758%26arnumber%3D4418778 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561828 Wed, 02 Jul 2008 12:36:17 +0100 1561828 http://www.medworm.com/index.php?rid=1561827&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418777.pdf%3Fisnumber%3D4418758%26arnumber%3D4418777 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561827 Wed, 02 Jul 2008 12:36:17 +0100 1561827 http://www.medworm.com/index.php?rid=1561826&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418776.pdf%3Fisnumber%3D4418758%26arnumber%3D4418776 Contributing editor Francis Sullivan describes the effects the Web--specifically, sites like Google and Amazon--have had, good and bad, on scientific research. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561826 Wed, 02 Jul 2008 12:36:17 +0100 1561826 http://www.medworm.com/index.php?rid=1561825&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418775.pdf%3Fisnumber%3D4418758%26arnumber%3D4418775 Careers in science and engineering entail interactions with professionals from many fields. Interdisciplinary work in graduate school—such as that found at UMBC’s Center for Interdisciplinary Research and Consulting— offer a way for students to gain experience with handling the challenges involved in these interactions. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561825 Wed, 02 Jul 2008 12:36:17 +0100 1561825 http://www.medworm.com/index.php?rid=1561824&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418774.pdf%3Fisnumber%3D4418758%26arnumber%3D4418774 Direct volume rendering is an effective method for plotting 3D scientific data, but it’s not used as frequently as it could be. Here, the authors summarize direct volume rendering and discuss barriers to taking advantage of this powerful technique. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561824 Wed, 02 Jul 2008 12:36:17 +0100 1561824 http://www.medworm.com/index.php?rid=1561823&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418773.pdf%3Fisnumber%3D4418758%26arnumber%3D4418773 To set up a mock data challenge, the authors needed to string together a lot of existing and new code. Here, they describe how Python and XML came to the rescue. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561823 Wed, 02 Jul 2008 12:36:17 +0100 1561823 http://www.medworm.com/index.php?rid=1561822&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418772.pdf%3Fisnumber%3D4418758%26arnumber%3D4418772 Spin dynamics methods can provide insight into excitations and dynamic critical behavior of magnetic systems and can now enable the study of such systems with a precision that equals or exceeds that of experiment. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561822 Wed, 02 Jul 2008 12:36:17 +0100 1561822 http://www.medworm.com/index.php?rid=1561821&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418771.pdf%3Fisnumber%3D4418758%26arnumber%3D4418771 Contributing editor Paul F. Dubois talks about a programming sprint in which he recently participated. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561821 Wed, 02 Jul 2008 12:36:17 +0100 1561821 http://www.medworm.com/index.php?rid=1561820&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418770.pdf%3Fisnumber%3D4418758%26arnumber%3D4418770 The generic programming facilities of C++ allow the creation of efficient yet flexible computational systems. The Diagon framework describes the computation of energies and states for general quantum nanoscopic systems. Specifically, it uses the configuration interaction method to obtain all the many-body correlations of the system. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561820 Wed, 02 Jul 2008 12:36:17 +0100 1561820 http://www.medworm.com/index.php?rid=1561819&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418769.pdf%3Fisnumber%3D4418758%26arnumber%3D4418769 The method described here separates signal (trend) from noise in a set of measured bivariate data when there is no mathematical model for that signal. A computer program called spline2 implements the algorithm, which the authors apply to laboratory and real-world example problems. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561819 Wed, 02 Jul 2008 12:36:17 +0100 1561819 http://www.medworm.com/index.php?rid=1561818&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418768.pdf%3Fisnumber%3D4418758%26arnumber%3D4418768 Using a database management system (DBMS) is essential to ensure the data integrity and reliability of large, multidimensional data sets. However, loading multiterabyte data into a DBMS is a time-consuming and error-prone task that the authors have tried to automate by developing the sqlLoader pipeline—a distributed workflow system for data loading. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561818 Wed, 02 Jul 2008 12:36:17 +0100 1561818 http://www.medworm.com/index.php?rid=1561817&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418767.pdf%3Fisnumber%3D4418758%26arnumber%3D4418767 The multiterabyte Sloan Digital Sky Survey’s (SDSS’s) catalog data is stored in a commercial relational database management system with SQL query access and a built-in query optimizer. The SDSS Catalog Archive Server adds advanced data mining features to the DBMS to provide fast online access to the data. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561817 Wed, 02 Jul 2008 12:36:17 +0100 1561817 http://www.medworm.com/index.php?rid=1561816&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418766.pdf%3Fisnumber%3D4418758%26arnumber%3D4418766 Catalog Archive Server Jobs (CasJobs) is an asynchronous query workbench service that lets users run unrestricted SQL queries against scientific catalog archives. After running queries in batch mode, users can save their results to a personal database called MyDB before downloading them, letting users manage their query workloads, results, and histories without causing network overloads. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561816 Wed, 02 Jul 2008 12:36:17 +0100 1561816 http://www.medworm.com/index.php?rid=1561815&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418765.pdf%3Fisnumber%3D4418758%26arnumber%3D4418765 This article discusses challenges in public distribution of data of this complexity and how the project addressed them. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561815 Wed, 02 Jul 2008 12:36:17 +0100 1561815 http://www.medworm.com/index.php?rid=1561814&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418764.pdf%3Fisnumber%3D4418758%26arnumber%3D4418764 The Sloan Digital Sky Survey Science Archive represents a thousand-fold increase in the total amount of data that astronomers have collected to date. The pioneering instrumentation technology that made this possible is matched by groundbreaking tools that let anyone in the world access terabytes of SDSS data online. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561814 Wed, 02 Jul 2008 12:36:17 +0100 1561814 http://www.medworm.com/index.php?rid=1561813&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418763.pdf%3Fisnumber%3D4418758%26arnumber%3D4418763 Take a look around for textbooks explaining the foundations of bioinformatics to advanced undergraduates and you'll find a very limited selection. Luckily, at least one textbook fills the niche nicely and provides an excellent launching pad for undergraduates ready to begin using in silico and high throughput biology. Now in its second edition, Discovering Genomics, Proteomics, and Bioinformatics by A. Malcolm Campbell and Laurie J. Heyer offers a biology-centered, problem-solving approach to tackling this growing and rapidly evolving discipline. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561813 Wed, 02 Jul 2008 12:36:17 +0100 1561813 http://www.medworm.com/index.php?rid=1561812&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418762.pdf%3Fisnumber%3D4418758%26arnumber%3D4418762 CiSE's editor in chief, Norman Chonacky, describes some recent events that underscore the relevance of CiSE's mission. This piece also features an interview with the magazine's cover artist, Dirk Hagner. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561812 Wed, 02 Jul 2008 12:36:17 +0100 1561812 http://www.medworm.com/index.php?rid=1561811&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418761.pdf%3Fisnumber%3D4418758%26arnumber%3D4418761 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561811 Wed, 02 Jul 2008 12:36:17 +0100 1561811 http://www.medworm.com/index.php?rid=1561810&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418760.pdf%3Fisnumber%3D4418758%26arnumber%3D4418760 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561810 Wed, 02 Jul 2008 12:36:17 +0100 1561810 http://www.medworm.com/index.php?rid=1561809&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5992%2F4418758%2F04418759.pdf%3Fisnumber%3D4418758%26arnumber%3D4418759 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1561809 Wed, 02 Jul 2008 12:36:17 +0100 1561809 http://www.medworm.com/index.php?rid=1557940&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488073 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557940 Tue, 01 Jul 2008 12:21:22 +0100 1557940 http://www.medworm.com/index.php?rid=1557939&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488072 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557939 Tue, 01 Jul 2008 12:21:22 +0100 1557939 http://www.medworm.com/index.php?rid=1557938&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488071 Columnist Francis Sullivan ponders the mysteries of Gmail, and talks about the trade-offs between what it promises and the costs of those promises. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557938 Tue, 01 Jul 2008 12:21:22 +0100 1557938 http://www.medworm.com/index.php?rid=1557937&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488070 The heart of the Sony PlayStation 3, the STI CELL processor, wasn't originally intended for scientific number crunching, just as the PlayStation 3 itself wasn't meant primarily to serve such purposes. Yet, both these items could impact the high-performance computing world. This introductory article takes a closer look at the cause of this potential disturbance. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557937 Tue, 01 Jul 2008 12:21:22 +0100 1557937 http://www.medworm.com/index.php?rid=1557936&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488069 With the help of domain-driven development frameworks such as Naked Objects for Java, changes to an application's core functionality propagate automatically to the user interface and persistence layers. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557936 Tue, 01 Jul 2008 12:21:22 +0100 1557936 http://www.medworm.com/index.php?rid=1557935&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488068 Wave propagation is a phenomenon of fundamental importance to a wide variety of problems involving disordered media; numerical simulation is the only practical way of studying it. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557935 Tue, 01 Jul 2008 12:21:22 +0100 1557935 http://www.medworm.com/index.php?rid=1557934&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488067 Javier E. Hasbun reviews Christof Koch's Biophysics of Computation: Information Processing in Single Neurons. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557934 Tue, 01 Jul 2008 12:21:22 +0100 1557934 http://www.medworm.com/index.php?rid=1557933&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488066 Over the course of a three-part series, the authors will walk through the implementation of a simple but computationally intensive algorithm and show how a series of incremental refinements to the code yields significant performance gains. In this first installment, they concentrate on instruction selection and scheduling. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557933 Tue, 01 Jul 2008 12:21:22 +0100 1557933 http://www.medworm.com/index.php?rid=1557932&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488065 The authors introduce an ocean observatory, offer a vision of observatory-enabled scientific exploration, and discuss the requirements and approaches for generating provenance-aware products in such environments. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557932 Tue, 01 Jul 2008 12:21:22 +0100 1557932 http://www.medworm.com/index.php?rid=1557931&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488064 Provenance information can be seen as a pyramid with four main levels: data, organization, process, and knowledge. The first three levels focus on how data is transformed across a process's execution, the roles of the actors involved, and which tasks it comprises. However, the increasing complexity of the distributed, data-intensive applications that produce ever-larger amounts of provenance information require more advanced analytical capabilities with a higher level of abstraction. In this regard, the authors approach knowledge provenance as being focused on providing users with meaningful interpretations of process executions, explaining provenance in a way closer to how domain experts reason on a given problem, and facilitating their comprehension. Their approach is based on problem-so... Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557931 Tue, 01 Jul 2008 12:21:22 +0100 1557931 http://www.medworm.com/index.php?rid=1557930&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488063 Current scientific applications are often structured as workflows and rely on workflow systems to compile abstract experiment designs into enactable workflows that utilize the best available resources. The automation of this step, and of the workflow enactment, hides the details about how results are produced. Knowing how compilation and enactment occurred allows results to be reconnected with the experiment design. The authors investigate how provenance helps scientists connect their results with the actual execution that took place, their original experiment, and its inputs and parameters. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557930 Tue, 01 Jul 2008 12:21:22 +0100 1557930 http://www.medworm.com/index.php?rid=1557929&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488062 Provenance—the logging of information about how data came into being and how it was processed—is an essential aspect of managing large-scale simulation and data-intensive projects. Using a cosmology code comparison project as an example, this article presents how a provenance system can play a key role in such applications. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557929 Tue, 01 Jul 2008 12:21:22 +0100 1557929 http://www.medworm.com/index.php?rid=1557928&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488061 The adoption of large-scale distributed computing for high-energy physics presents new opportunities and challenges for physicists analyzing the data from the Large Hadron Collider experiments. With petabytes of data to manage, accessed by thousands of systems and used by thousands of collaborators, effective provenance is critical to the understanding of how the physics results were produced. In this article, the authors discuss several uses of data provenance in high-energy physics workflows and the opportunities for improvements in data analysis workflows that result from decentralized provenance collection and fine-grained object annotations. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557928 Tue, 01 Jul 2008 12:21:22 +0100 1557928 http://www.medworm.com/index.php?rid=1557927&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488060 The problem of systematically capturing and managing provenance for computational tasks has recently received significant attention because of its relevance to a wide range of domains and applications. The authors give an overview of important concepts related to provenance management, so that potential users can make informed decisions when selecting or designing a provenance solution. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557927 Tue, 01 Jul 2008 12:21:22 +0100 1557927 http://www.medworm.com/index.php?rid=1557926&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488059 Systematic mechanisms for capturing and exploring lineage information of digital artifacts are at the heart of a new field of research called computational provenance. This special issue aims to raise awareness and contribute to a better understanding of the issues surrounding computational provenance to the broader CiSE community. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557926 Tue, 01 Jul 2008 12:21:22 +0100 1557926 http://www.medworm.com/index.php?rid=1557925&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488058 Columnist Paul F. Dubois looks at some of the dangers of modern life, including cell phones and their ilk. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557925 Tue, 01 Jul 2008 12:21:22 +0100 1557925 http://www.medworm.com/index.php?rid=1557924&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488057 Much of today's thinking about computational science education is shaped by the needs of the high-performance minority and the perspective of academic computer science. What most working scientists actually need is basic software development skills. Focusing attention on this will be the best way to make the long-promised computational revolution a reality. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557924 Tue, 01 Jul 2008 12:21:22 +0100 1557924 http://www.medworm.com/index.php?rid=1557923&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488056 Editor-in-chief Norman Chonacky draws attention to Greg Wilson's argument that we aren't preparing students to be computationalists who will be able to call their work science. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557923 Tue, 01 Jul 2008 12:21:22 +0100 1557923 http://www.medworm.com/index.php?rid=1557922&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488055 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557922 Tue, 01 Jul 2008 12:21:22 +0100 1557922 http://www.medworm.com/index.php?rid=1557921&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488054 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557921 Tue, 01 Jul 2008 12:21:22 +0100 1557921 http://www.medworm.com/index.php?rid=1557920&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D4488052%26arnumber%3D4488053 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=1557920 Tue, 01 Jul 2008 12:21:22 +0100 1557920 http://www.medworm.com/index.php?rid=2628236&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5076307%26arnumber%3D5076313 Norman Chonacky reviews Computation in Modern Physics. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2628236 Thu, 01 Jan 1970 00:00:00 +0100 2628236 http://www.medworm.com/index.php?rid=2491252&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5076307%26arnumber%3D5076329 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2491252 Thu, 01 Jan 1970 00:00:00 +0100 2491252 http://www.medworm.com/index.php?rid=2491251&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5076307%26arnumber%3D5076328 (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2491251 Thu, 01 Jan 1970 00:00:00 +0100 2491251 http://www.medworm.com/index.php?rid=2491250&cid=s_37224_21_f&fid=37224&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5076307%26arnumber%3D5076327 Columnist Charles Day compares the experience of digitized medical records vs. paper versions in two recent trips—one to the vet's office for his dog, Gemma, and the other to his own doctor's office for a personal checkup. (Source: Computing in Science and Engineering) Computing in Science and Engineering journals http://www.medworm.com/rss/comments.php?id=2491250 Thu, 01 Jan 1970 00:00:00 +0100 2491250