Increasingly complex research has made it more difficult to prepare data for publication, education, and outreach. Many scientists must also wade through black-box code to interface computational algorithms from diver...
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Increasingly complex research has made it more difficult to prepare data for publication, education, and outreach. Many scientists must also wade through black-box code to interface computational algorithms from diverse sources to supplement their bench work. To reduce these barriers we have developed an open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (hosts) to provide simultaneous access to the capabilities of these newly connected systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease. By enabling easy exchange of algorithms, ePMV can facilitate interdisciplinary research, smooth communication between broadly diverse specialties, and provide a common platform to frame and visualize the increasingly detailed intersection(s) of cellular and molecular biology.
In this paper, a method of creating a Three-Dimensional (3-D) face image from one or more 2-D face images is proposed. The 3-D synthetic face is actually represented by parameters of a set of 3-D face images of other ...
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In this paper, a method of creating a Three-Dimensional (3-D) face image from one or more 2-D face images is proposed. The 3-D synthetic face is actually represented by parameters of a set of 3-D face images of other persons. When a 2-D probing photo is presented, a 3-D synthetic face image is projected onto the 2-D image plane, following the pose and illumination compensations. An optimisation algorithm is applied to minimise the error, once the algorithm converges, the depth and intensity parameters of the 3-D synthetic face image are obtained of the 2-D probing photo in the 3-D space.
Motivation: Infectious disease research is generating an increasing amount of disparate data on pathogenic systems. There is a growing need for resources that effectively integrate, analyze, deliver and visualize thes...
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Motivation: Infectious disease research is generating an increasing amount of disparate data on pathogenic systems. There is a growing need for resources that effectively integrate, analyze, deliver and visualize these data, both to improve our understanding of infectious diseases and to facilitate the development of strategies for disease control and prevention. Results: We have developed Disease View, an online host-pathogen resource that enables infectious disease-centric access, analysis and visualization of host-pathogen interactions. In this resource, we associate infectious diseases with corresponding pathogens, provide information on pathogens, pathogen virulence genes and the genetic and chemical evidences for the human genes that are associated with the diseases. We also deliver the relationships between pathogens, genes and diseases in an interactive graph and provide the geolocation reports of associated diseases around the globe in real time. Unlike many other resources, we have applied an iterative, user-centered design process to the entire resource development, including data acquisition, analysis and visualization.
We are all faced with uncertainty about the future, but we can get the measure of some uncertainties in terms of probabilities. Probabilities are notoriously difficult to communicate effectively to lay audiences, and ...
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We are all faced with uncertainty about the future, but we can get the measure of some uncertainties in terms of probabilities. Probabilities are notoriously difficult to communicate effectively to lay audiences, and in this review we examine current practice for communicating uncertainties visually, using examples drawn from sport, weather, climate, health, economics, and politics. Despite the burgeoning interest in infographics, there is limited experimental evidence on how different types of visualizations are processed and understood, although the effectiveness of some graphics clearly depends on the relative numeracy of an audience. Fortunately, it is increasingly easy to present data in the form of interactive visualizations and in multiple types of representation that can be adjusted to user needs and capabilities. Nonetheless, communicating deeper uncertainties resulting from incomplete or disputed knowledge-or from essential indeterminacy about the future-remains a challenge.
Motivation: Networks and pathways are important in describing the collective biological function of molecular players such as genes or proteins. In many areas of biology, for example in cancer studies, available data ...
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Motivation: Networks and pathways are important in describing the collective biological function of molecular players such as genes or proteins. In many areas of biology, for example in cancer studies, available data may harbour undiscovered subtypes which differ in terms of network phenotype. That is, samples may be heterogeneous with respect to underlying molecular networks. This motivates a need for unsupervised methods capable of discovering such subtypes and elucidating the corresponding network structures. Results: We exploit recent results in sparse graphical model learning to put forward a 'network clustering' approach in which data are partitioned into subsets that show evidence of underlying, subset-level network structure. This allows us to simultaneously learn subset-specific networks and corresponding subset membership under challenging small-sample conditions. We illustrate this approach on synthetic and proteomic data.
This paper introduces a novel technique to create digital potteries using certain number-theoretic techniques of digital geometry. Given a digital generatrix, the proposed wheel-throwing procedure works with a few pri...
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This paper introduces a novel technique to create digital potteries using certain number-theoretic techniques of digital geometry. Given a digital generatrix, the proposed wheel-throwing procedure works with a few primitive integer computations only, wherein lies its strength and novelty. The digital surface created out of the digital wheel-throwing is digitally connected and irreducible when the digital generatrix is an irreducible digital curve segment, which ensures its successful rendition with a realistic finish, whatsoever may be the zoom factor. The proposed technique is also bestowed with the desired quality of producing a monotone or a non-monotone digital surface of revolution depending on whether or not the digital generatrix is monotone with respect to the axis of revolution. Thick-walled potteries, therefore, can be created successfully and efficiently to have the final product ultimately resembling a real-life pottery. Experimental results with some typical generatrices demonstrate its efficiency, elegance and versatility.
Motivation: Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus. Analyzing the data from FISH images is a tedious process t...
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Motivation: Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus. Analyzing the data from FISH images is a tedious process that invokes an element of subjectivity. Automated FISH image analysis offers savings in time as well as gaining the benefit of objective data analysis. While several FISH image analysis software tools have been developed, they often use a threshold- based segmentation algorithm for nucleus segmentation. As fluorescence signal intensities can vary significantly from experiment to experiment, from cell to cell, and within a cell, threshold- based segmentation is inflexible and often insufficient for automatic image analysis, leading to additional manual segmentation and potential subjective bias. To overcome these problems, we developed a graphical software tool called FISH Finder to automatically analyze FISH images that vary significantly. By posing the nucleus segmentation as a classification problem, compound Bayesian classifier is employed so that contextual information is utilized, resulting in reliable classification and boundary extraction. This makes it possible to analyze FISH images efficiently and objectively without adjustment of input parameters. Additionally, FISH Finder was designed to analyze the distances between differentially stained FISH probes.
Daniela K. Rosner discusses how in the San Francisco Bay Area, large festivals like Burning Man and Maker Faire, teaching facilities like the Crucible and Center for the Book, as well as independent studios and hacker...
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Daniela K. Rosner discusses how in the San Francisco Bay Area, large festivals like Burning Man and Maker Faire, teaching facilities like the Crucible and Center for the Book, as well as independent studios and hacker spaces energize a surprising range of personal, 'by hand' production. People engage in handwork as a response to, and an extension of, the technological culture in which they are embedded. Mike has a background in chemistry, computer graphics, and engineering, and spent most of his professional career using software tools to design hardware. Out of the kiln, the vases allow Mike to formulate his understanding of how the chemicals and the shape of the clay play together with heat. Mike learns through experimentation with the numerous test tiles he creates before the full vase. The digital amalgam of online documents is therefore seen as different from the physical book.
Real fluid phenomena often present multi-scale behavior,such as tiny splashes and foams in the ocean and small vortexes near the bank of a wide river,which requires sufficiently fine grids and long computational time ...
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Real fluid phenomena often present multi-scale behavior,such as tiny splashes and foams in the ocean and small vortexes near the bank of a wide river,which requires sufficiently fine grids and long computational time in the simulation to get adequately resolved *** present a new method to address this issue by solving Navier-Stokes equation on multiple layers of grids with different resolutions or *** governing equations are solved on different layers in successive *** the velocity and pressure fields are synchronized between adjacent layers through the processes of prolongation and *** multi-layer approach enables combining the respective advantages of various grid types,catching the multi-scale behavior of fluids and optimizing the computational *** simple examples,the regular-tetrahedral and the coarse-fine bi-layer grids,are given to illustrate the powerfulness of the multi-layer framework.
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