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Showing papers in "Computing in Science and Engineering in 2007"


Journal ArticleDOI
TL;DR: Matplotlib is a 2D graphics package used for Python for application development, interactive scripting, and publication-quality image generation across user interfaces and operating systems.
Abstract: Matplotlib is a 2D graphics package used for Python for application development, interactive scripting,and publication-quality image generation across user interfaces and operating systems

23,312 citations


Journal Article
TL;DR: Python is an excellent "steering" language for scientific codes written in other languages, but with additional basic tools, it transforms into a high-level language suited for scientific and engineering code that's often fastenough to be immediately useful but also flexible enough to be sped up with additional extensions.
Abstract: Python is an excellent "steering" language for scientific codes written in other languages. However, with additional basic tools, Python transforms into a high-level language suited for scientific and engineering code that's often fast enough to be immediately useful but also flexible enough to be sped up with additional extensions.

2,841 citations


Journal ArticleDOI
TL;DR: This survey introduces the application, implementation, and underlying principles of sensitivity and uncertainty quantification inredictive modeling.
Abstract: Predictive modeling's effectiveness is hindered by inherent uncertainties in the input parameters. Sensitivity and uncertainty analysis quantify these uncertainties and identify the relationships between input and output variations, leading to the construction of a more accurate model. This survey introduces the application, implementation, and underlying principles of sensitivity and uncertainty quantification

988 citations


Journal ArticleDOI
TL;DR: A package for analyzing magnetic resonance imaging (MRI) and functional MRI (fMRI) data is described, which is part of the Neuroimaging in Python (NIPY) project.
Abstract: The authors describe a package for analyzing magnetic resonance imaging (MRI) and functional MRI (fMRI) data, which is part of the Neuroimaging in Python (NIPY) project. An international group of leading statisticians, physicists, programmers, and neuroimaging methodologists ore developing NIPY for wider use

83 citations


Journal ArticleDOI
TL;DR: A new Bayesian-analysis-based region-growing algorithm for medical image segmentation that can robustly and effectively segment medical images is discussed, and experimental results show that the approach is reliable and efficient.
Abstract: This paper discusses a new Bayesian-analysis-based region-growing algorithm for medical image segmentation that can robustly and effectively segment medical images. Specifically the approach studies homogeneity criterion parameters in a local neighbor region. Using the multislices Gaussian and anisotropic filters as a preprocess helps reduce an image's noise. The algorithm framework is tested on CT and MRI image segmentation, and experimental results show that the approach is reliable and efficient.

78 citations


Journal ArticleDOI
TL;DR: Making the most of multicore systems will require new tools, new algorithms, and a new way of looking at programming, says Georgia Tech professor David A. Bader.
Abstract: There's no question that multicore processors have gone mainstream. These computer chips, which have more than one CPU, first hit the consumer market less than two years ago. Today, practically every new computer has a dual-core (two-CPU) chip, and Intel just launched a quad-core chip with four CPUs. One of 2006's most in-demand holiday gifts was Sony's PlayStation 3, which boasts a "cell" chip with nine CPUs for faster and more realistic video gaming. Multicore systems might offer advantages to gamers, but what about researchers? David A. Bader, who directs a new research center at Georgia Tech devoted to cell technology, says that making the most of multicore systems will require new tools, new algorithms, and a new way of looking at programming

78 citations


Journal ArticleDOI
TL;DR: CompuCell3D is presented, a multitiered, flexible, and scalable problem-solving environment for morphogenesis simulations that's written in C++ using object-oriented design patterns.
Abstract: To gain performance, developers often build scientific applications in procedural languages, such as C or Fortran, which unfortunately reduces flexibility. To address this imbalance, the authors present CompuCell3D, a multitiered, flexible, and scalable problem-solving environment for morphogenesis simulations that's written in C++ using object-oriented design patterns.

61 citations


Journal ArticleDOI
TL;DR: SloopCell as mentioned in this paper is an open source software system to model biomolecular reaction networks, which is written in Python and uses third-party libraries extensively, but also does some fun things with on-the-fly code generation and parallel programming.
Abstract: Researchers at Cornell University have built an open source software system to model biomolecular reaction networks. SloppyCell is written in Python and uses third-party libraries extensively, but it also does some fun things with on-the-fly code generation and parallel programming.

58 citations


Journal ArticleDOI
TL;DR: To understand dynamic mechanisms, scientists need intuitive and convenient ways to validate known relationships and reveal hidden ones among multiple variables.
Abstract: To understand dynamic mechanisms, scientists need intuitive and convenient ways to validate known relationships and reveal hidden ones among multiple variables

53 citations


Journal ArticleDOI
TL;DR: The authors present examples of stochastic simulations of compressible and incompressible flows and provide analytical solutions for verifying these newly emerging methods for stochastically modeling.
Abstract: Stochastic simulations in computational fluid dynamics let researchers model uncertainties beyond numerical discretization errors. The authors present examples of stochastic simulations of compressible and incompressible flows and provide analytical solutions for verifying these newly emerging methods for stochastic modeling

42 citations


Journal ArticleDOI
TL;DR: The Python motto "batteries included" is meant to convey the idea that Python comes with everything you need.
Abstract: Our special theme this issue is the computer programming language Python and the increasing role it plays in scientific projects. Free and universally available, Python comes with a vast standard library containing support for nearly every area of computer science. An even more extensive set of third-party tools and modules covers additional tasks, from managing a Web site to doing a fast Fourier transform to distributed or parallel programming. The Python motto "batteries included" is meant to convey the idea that Python comes with everything you need.

Journal ArticleDOI
TL;DR: It is shown that Gauss-Vanick analysis of this diversity data detrended with a cubic also strongly signals a 62-million-year periodicity, and that the two techniques are equivalent.
Abstract: This article shows that Gauss-Vanick (GV) analysis of this diversity data detrended with a cubic also strongly signals a 62-million-year periodicity. Furthermore, it was found that neither GV analysis nor Fourier transform analysis of the nondetrended data leads to any statistically significant periodicity. The results show that the two techniques are equivalent.

Journal ArticleDOI
TL;DR: The combination of the Python language and the bulk synchronous parallel computing model make developing and testing parallel programs a much more pleasurable experience.
Abstract: The combination of the Python language and the bulk synchronous parallel computing model make developing and testing parallel programs a much more pleasurable experience.

Journal ArticleDOI
TL;DR: Among many computer scientists, fortran is an f-word, yet, it's still the most widely used language in scientific computing, especially when high performance is required.
Abstract: Among many computer scientists, fortran is an f-word. yet, it's still the most widely used language in scientific computing, especially when high performance is required. why is this so? One explanation often given is the huge amount of scientific legacy code in the world-after all, differential equations remain the same over time and so do their solvers, so there's no reason to rewrite such code. But a great deal of new code is written in Fortran95 as well. One of us recently served on a review panel for granting computer time to high-impact scientific computing applications that effectively use thousands of processors, and every single one of the applications he reviewed was written in Fortran. At last year's conference on computational physics in South Korea (CCP2006), most of the plenary speakers who talked about codes used Fortran. Perhaps scientists prefer Fortran because they're productive when using it.

Journal ArticleDOI
TL;DR: Two Python modules for solving partial differential equations (PDEs) are described: PyCC is designed as a Matlab-like environment for writing algorithms for solving PDEs, and SyFi creates matrices based on symbolic mathematics, code generation, and the finite element method.
Abstract: This article describes two Python modules for solving partial differential equations (PDEs): PyCC is designed as a Matlab-like environment for writing algorithms for solving PDEs, and SyFi creates matrices based on symbolic mathematics, code generation, and the finite element method.

Journal ArticleDOI
TL;DR: Simulations showed a dramatic increase in the range of magnetic field in which the magnetron functions, a doubling of output power, an increase in efficiency, an elimination of mode competition, and halving of the startup time.
Abstract: Shaped cathodes enhance key magnetron performance parameters, such as output power, power efficiency, and impedance. Simulations using these novel designs showed a dramatic increase in the range of magnetic field in which the magnetron functions, a doubling of output power, an increase in efficiency, an elimination of mode competition, and halving of the startup time.

Journal ArticleDOI
TL;DR: The authors give a simple, efficient, and easy-to-implement prescription for numerically evaluating finite Hilbert transforms.
Abstract: The authors give a simple, efficient, and easy-to-implement prescription for numerically evaluating finite Hilbert transforms.

Journal ArticleDOI
TL;DR: The authors' interdisciplinary computational methods course uses Python and associated numerical and visualization libraries to enable students to implement simulations for several different course modules, which highlight the breadth and flexibility of Python-powered computational environments.
Abstract: The authors' interdisciplinary computational methods course uses Python and associated numerical and visualization libraries to enable students to implement simulations for several different course modules, which highlight the breadth and flexibility of Python-powered computational environments.

Journal ArticleDOI
TL;DR: Educators at an institution in Germany have started using Python to teach computational physics, and the author describes how graphical visualizations also play an important role, which he illustrates here with a few simple examples.
Abstract: Educators at an institution in Germany have started using Python to teach computational physics. The author describes how graphical visualizations also play an important role, which he illustrates here with a few simple examples

Journal ArticleDOI
TL;DR: The authors focus on the measurement and time evolution of two-state superpositions in the context of bound states and spin.
Abstract: Much of the difficulty in learning advanced concepts in quantum mechanics comes from trying to visualize abstract problems. This article addresses the situation with interactive curricular material created as part of the open source physics project. In particular, the authors focus on the measurement and time evolution of two-state superpositions in the context of bound states and spin.

Journal ArticleDOI
TL;DR: The method for volume visualization of tissue-level intermixing at a microscopic scale reveals differences between the specimens that aren't obvious in a stack of 2D images alone.
Abstract: The authors examine phenotype differences in wildtype and retinoblastoma (Rb) knockout specimens of mouse placenta. Their method for volume visualization of tissue-level intermixing at a microscopic scale reveals differences between the specimens that aren't obvious in a stack of 2D images alone

Journal ArticleDOI
TL;DR: In this article, a dual-lookup table transfer function was proposed to improve the visualization of fused PET/CT renderings, which can be used to enhance the performance of computed tomography/computed tomography rendering.
Abstract: In positron emission tomography/computed tomography (PET/CT) volume rendering, volume images are associated with individual lookup tables, which users must manipulate independently of the resultant volumes being fused. An intuitive, efficient dual-lookup table transfer function can improve the visualization of fused PET/CT renderings

Journal ArticleDOI
TL;DR: This introduction to the theme issue explores how the DoD's computational systems have contributed to various scientific works.
Abstract: The US Department of Defense is reducing its dependence on the traditional "design, build, break, and fix" paradigm for designing and testing weapons systems by supplementing empirical testing with computational science and engineering. This introduction to the theme issue explores how the DoD's computational systems have contributed to various scientific works.

Journal ArticleDOI
TL;DR: An effective, robust, and fast loop-detection strategy for creating evenly spaced streamlines is described, which allows interactive streamline placement for complex flows on an ordinary PC.
Abstract: The authors present a robust and fast loop-detection strategy to interactively place dense, uncluttered, evenly spaced streamlines, which help visualize complex flows. Although loop detection is critical to streamline placement, few researchers have addressed this issue. In this paper an effective, robust, and fast loop-detection strategy for creating evenly spaced streamlines is described. At a negligible additional cost, it allows interactive streamline placement for complex flows on an ordinary PC.

Journal ArticleDOI
TL;DR: Some key problems in resource management that represent opportunities for computer scientists and engineers in search of challenging practical problems are highlighted.
Abstract: Recent advances in miniaturization, computing power, remote sensing, and modeling are revolutionizing the science of natural resource management, but these advances also bring many challenges. This article highlights some key problems in resource management that represent opportunities for computer scientists and engineers in search of challenging practical problems.

Journal ArticleDOI
TL;DR: The author describes how Python has helped scientists calibrate and analyze data from the Hubble Space Telescope, first as a means of scripting legacy applications, and, more recently, as a way of developing new applications in Python itself.
Abstract: The author describes how Python has helped scientists calibrate and analyze data from the Hubble Space Telescope, first as a means of scripting legacy applications, and, more recently, as a way of developing new applications in Python itself.

Journal ArticleDOI
TL;DR: A nonphotorealistic rendering technique can help medical practitioners visualize anatomic models and illustrate them with different stylizations, and additional stroke texture synthesis enriches medical object illustrations.
Abstract: A nonphotorealistic rendering (NPR) technique can help medical practitioners visualize anatomic models and illustrate them with different stylizations. This technique provides potentially useful rendering alternatives to conventional volume or surface rendering in medical visualization. Improved performance allows interactive visualization of anatomic models, and additional stroke texture synthesis enriches medical object illustrations

Journal ArticleDOI
TL;DR: Quantum computing, say its champions, promises prodigious power, but in principle these algorithms can perform calculations far beyond classical computing's conceivable reach
Abstract: Quantum computing, say its champions, promises prodigious power. its basic currency, the qubit, exists in an on/off limbo until it's read out, so if you could operate on kqubits, a potentially vast space of 2 k values opens up for computation. the fundamental operation on qubits is a rotation. Combine the rotations, and you have logic gates. Combine the logic gates, and you have algorithms. In principle, these algorithms can perform calculations far beyond classical computing's conceivable reach

Journal ArticleDOI
TL;DR: The authors describe how they use Python for nanophotonics research-specifically using it for electromagnetic modeling, mask design, and process simulation.
Abstract: The authors describe how they use Python for nanophotonics research-specifically, they describe using it for electromagnetic modeling, mask design, and process simulation

Journal ArticleDOI
TL;DR: An important class of systems - billiards - can show a wide variety of dynamical behavior, and using tools developed in Python, researchers can interactively study the complexity of these dynamics.
Abstract: An important class of systems - billiards - can show a wide variety of dynamical behavior. Using tools developed in Python, researchers can interactively study the complexity of these dynamics. Such behavior is directly reflected in properties of the corresponding quantum systems, such as eigenvalue statistics or the structure of eigenfunctions