Motivation: Feedback circuits are important motifs in biological networks and part of virtually all regulation processes that are needed for a reliable functioning of the cell. Mathematically, feedback is connected to...
详细信息
Motivation: Feedback circuits are important motifs in biological networks and part of virtually all regulation processes that are needed for a reliable functioning of the cell. Mathematically, feedback is connected to complex behavior of the systems, which is often related to bifurcations of fixed points. Therefore, several approaches for the investigation of fixed points in biological networks have been developed in recent years. Many of them assume the fixed point coordinates to be known, and an efficient way to calculate the entire set of fixed points for interrelated feedback structures is highly desirable. Results: In this article, we consider regulatory network models, which are differential equations with an underlying directed graph that illustrates independencies among variables. We introduce the circuit-breaking algorithm (CBA), a method that constructs one-dimensional characteristics for these network models, which inherit important information about the system. In particular, fixed points are related to the zeros of these characteristics. The CBA operates on the graph topology, and results from graph theory are used in order to make calculations efficient. Our framework provides a general scheme for analyzing network models in terms of interrelated feedback circuits. The efficiency of the approach is demonstrated on a model for calcium oscillations based on experiments in hepatocytes, which consists of several interrelated feedback circuits.
Motivation: De novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific typ...
详细信息
Motivation: De novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific type of sequencing data. The number of known genomes is expanding rapidly, therefore it becomes possible to use multiple reference genomes for assembly projects. We introduce an assembly integrator that makes use of all available data, i.e. multiple de novo assemblies and mappings against multiple related genomes, by optimizing a weighted combination of criteria. Results: The developed algorithm was applied on the de novo sequencing of the Saccharomyces cerevisiae CEN. PK 113-7D strain. Using Solexa and 454 read data, two de novo and three comparative assemblies were constructed and subsequently integrated, yielding 29 contigs, covering more than 12 Mbp;a drastic improvement compared with the single assemblies.
Polynomial Texture Mapping is an image capture and processing technique that was developed by HP Labs in 2000. It enables the recording and representation of subtle surface details using a standard digital camera and ...
详细信息
Polynomial Texture Mapping is an image capture and processing technique that was developed by HP Labs in 2000. It enables the recording and representation of subtle surface details using a standard digital camera and lighting, and software that is free for non-commercial use. Cultural heritage applications have been associated with the technology from its earliest stages, including examples in areas such as cuneiform, numismatics, rock art, lithics and Byzantine art. The paper begins by outlining the technical principles involved. It then brings together the extant work in the field. Through examples developed by the University of Southampton in partnership with a range of UK and international bodies it demonstrates the benefits of the technology in the areas of archaeological analysis, conservation and representation. Finally it considers the future possibilities of this technology and ongoing developments. (C) 2010 Elsevier Ltd. All rights reserved.
Motivation: Protein sequences are often composed of regions that have distinct evolutionary histories as a consequence of domain shuffling, recombination or gene conversion. New approaches are required to discover, vi...
详细信息
Motivation: Protein sequences are often composed of regions that have distinct evolutionary histories as a consequence of domain shuffling, recombination or gene conversion. New approaches are required to discover, visualize and analyze these sequence regions and thus enable a better understanding of protein evolution. Results: Here, we have developed an alignment-free and visual approach to analyze sequence relationships. We use the number of shared n-grams between sequences as a measure of sequence similarity and rearrange the resulting affinity matrix applying a spectral technique. Heat maps of the affinity matrix are employed to identify and visualize clusters of related sequences or outliers, while n-gram-based dot plots and conservation profiles allow detailed analysis of similarities among selected sequences. Using this approach, we have identified signatures of domain shuffling in an otherwise poorly characterized family, and homology clusters in another. We conclude that this approach may be generally useful as a framework to analyze related, but highly divergent protein sequences. It is particularly useful as a fast method to study sequence relationships prior to much more time-consuming multiple sequence alignment and phylogenetic analysis.
This paper presents an interactive system for realistic visualization of earth-scale clouds. Realistic images can be generated at interactive frame rates while the viewpoint and the sunlight directions can be changed ...
详细信息
This paper presents an interactive system for realistic visualization of earth-scale clouds. Realistic images can be generated at interactive frame rates while the viewpoint and the sunlight directions can be changed interactively. The realistic display of earth-scale clouds requires us to render large volume data representing the density distribution of the clouds. However, this is generally time-consuming and it is difficult to achieve the interactive performance, especially when the sunlight direction can be changed. To address this, our system precomputes the integrated intensities and opacities of clouds for various viewing and sunlight directions. This idea is combined with a novel hierarchical data structure for further acceleration. The photorealism of the final image is improved by taking into account the atmospheric effects and shadows of clouds on the earth. We demonstrate the usefulness of our system by an application to a space flight simulation.
The creation of realistic 3D human body animations is one of the most challenging research topics of investigation in the domain of the 3D animation, as it constitutes an extremely time-consuming task that requires si...
详细信息
The creation of realistic 3D human body animations is one of the most challenging research topics of investigation in the domain of the 3D animation, as it constitutes an extremely time-consuming task that requires significant technical and creative expertise. The motivation of this research project is to develop a tool to simplify and automate the creation of human 3D movements by enhancing a 3D graphics creation tool. The proposed tool semi-automates the creation of human character animation, by specifying the starting and ending states and movement styles of a human avatar and the transitionary motion state between them.
Objective: Rigorous human-computer interaction (HCI) design methodologies have not traditionally been applied to the development of clinical trial participant tracking (CTPT) tools. Given the frequent use of iconic HC...
详细信息
Objective: Rigorous human-computer interaction (HCI) design methodologies have not traditionally been applied to the development of clinical trial participant tracking (CTPT) tools. Given the frequent use of iconic HCI models in CTPTs, and prior evidence of usability problems associated with the use of ambiguous icons in complex interfaces, such approaches may be problematic. Presentation Discovery (PD), a knowledge-anchored HCI design method, has been previously demonstrated to improve the design of iconic HCI models. In this study, we compare the usability of a CTPT HCI model designed using PD and an intuitively designed CTPT HCI model. Methods: An iconic CPTP HCI model was created using PD. The PD-generated and an existing iconic CTPT HCI model were subjected to usability testing, with an emphasis on task accuracy and completion times. Study participants also completed a qualitative survey instrument to evaluate subjective satisfaction with the two models. Results: CTPT end-users reliably and reproducibly agreed on the visual manifestation and semantics of prototype graphics generated using PD. The performance of the PD-generated iconic HCI model was equivalent to an existing HCI model for tasks at multiple levels of complexity, and in some cases superior. This difference was particularly notable when tasks required an understanding of the semantic meanings of multiple icons. Conclusion: The use of PD to design an iconic CTPT HCI model generated beneficial results and improved end-user subjective satisfaction, while reducing task completion time. Such results are desirable in information and time intensive domains, such as clinical trials management.
Crowd simulation has been an important research field due to its diverse range of applications that include film production, military simulation, and urban planning. A challenging problem is to provide simple yet effe...
详细信息
Crowd simulation has been an important research field due to its diverse range of applications that include film production, military simulation, and urban planning. A challenging problem is to provide simple yet effective control over captured and simulated crowds to synthesize intended group motions. We present a new method that blends existing crowd data to generate a new crowd animation. The new animation can include an arbitrary number of agents, extends for an arbitrary duration, and yields a natural-looking mixture of the input crowd data. The main benefit of this approach is to create new spatio-temporal crowd behavior in an intuitive and predictable manner. It is accomplished by introducing a morphable crowd model that allows us to encode the formations and individual trajectories in crowd data. Then, its original spatiotemporal behavior can be reconstructed and interpolated at an arbitrary scale using our morphable model.
Writing practices that integrate dynamic and interactive strategies into the making and reading of digital texts are proliferating as more of our reading experiences are mediated through the screen. We argue that rare...
详细信息
Writing practices that integrate dynamic and interactive strategies into the making and reading of digital texts are proliferating as more of our reading experiences are mediated through the screen. We argue that rarely do current approaches to creating digital texts operate at the basic textual level of the letterform itself, and that this neglect is partially due to the fact that current font technology is based on print paradigms that make it difficult to work programmatically at the level of individual letters. Work produced in our lab suggests the creative possibilities in being able to easily specify behaviours at such a level, and leads us to propose that writers, typographers and programmers start thinking beyond Postscript-like formats such as OpenType or TrueType to collaboratively develop a new ComplexType format (or formats) that is designed for the twenty-first century as opposed to a simulation of the fifteenth.
The intersection curve between two surfaces in three-dimensional real projective space RP(3) is important in the study of computer graphics and solid modelling. However, much of the past work has been directed towards...
详细信息
The intersection curve between two surfaces in three-dimensional real projective space RP(3) is important in the study of computer graphics and solid modelling. However, much of the past work has been directed towards the intersection of two quadric surfaces. In this paper we study the intersection curve between a quadric and a cubic surface and its projection onto the plane at infinity. Formulas for the plane and space curves are given for the intersection of a quadric and a cubic surface. A family of cubic surfaces that give the same space curve when we intersect them with a quadric surface is found. By generalizing the methods in Wang et al. (2002)[6] that are used to parametrize the space curve between two quadric surfaces, we give a parametrization for the intersection curve between a quadric and a cubic surface when the intersection has a singularity of order 3. (C) 2010 Elsevier B.V. All rights reserved.
暂无评论