Automatic Layouts Research Articles

Systematic cell placement in quantum‐dot cellular automata embedding underlying regular clocking circuit

Quantum-dot cellular automata (QCA) is gaining worldwide popularity due to its higher device concentration, lower power indulgence, and better switching speed. The information flows in QCA with the polarization state defined by the placement of electrons instead of current flow. The cell interaction principle under the influence of the clocking zone controls the cell placement during QCA circuit design. Most of the designs reported so far used random cell placement, which has no fabricating sense. Moreover, it is equally important for a cell placement algorithm to follow a realistic, regular underlying clocking scheme to maintain proper routing channels. In this regard, a systematic cell placement for the combinational logic circuit in QCA is proposed using the widely accepted underlying regular clocking scheme, universal, scalable and efficient (USE). The proposed method traverses all possible paths of a combinational logic circuit from output to input to build the desired circuit generating the automatic cell layout. A grid of clock zone of USE clock scheme is considered in the initial layout driving different paths of the circuit and finally evolves as the desired circuit. The generated automatic QCA layouts are competitive in occupied area, delay, and its cell count, which advocates the significance of such a scheme.

DancingWords: exploring animated word clouds to tell stories

By encoding semantic relations into relative positions, word clouds have shown the capability to deliver richer messages than purely visualizing word frequencies. Existing studies mainly focus on layout algorithms that cluster related words, preserve temporal coherence, and optimize spatial shapes. However, they cannot fully convey multiple relations among words and their evolvement through relative positions and static representations. In this paper, we explore animated word clouds that take advantage of storytelling strategies to present interactions between words and show the dynamic process of content changes, thus communicating the underlying stories. We initially create several exemplars of animated word clouds with designers through a structured iterative design process. These exemplars lead to a preliminary design space that distills essential narrative elements with design choices. Based on the design space, we develop a prototype tool, DancingWords, which provides story-oriented interactions and automatic layouts for users to generate animated word clouds. We evaluate the expressiveness and usefulness of our system through several example animated stories and a usability study with general users. The results show that DancingWords allows users to produce appealing storytelling videos easily and quickly for communication.

Implicit and explicit spatial-numerical representations diverge in number-form synesthetes.

In number-form (NF) synesthesia-a condition in which people report vivid, automatic and consistent mental layouts for numerical sequences-numbers and space are closely linked. These explicit associations are similar to the implicit associations demonstrated by the Spatial-Numerical Association of Response Codes (SNARC) effect. Thus, NF synesthesia offers a unique opportunity to investigate spatial-numerical associations. We tested implicit and explicit representations in NF synesthetes using a multiple case-study design. Over two sessions, synesthetes participated in a semi-structured interview focusing on the nature of their associations, as well as SNARC and number line estimation tasks. Contrary to our hypotheses, only one synesthete demonstrated SNARC effects congruent with her reported form, whereas two others exhibited SNARC effects that were the opposite of their explicit NFs. While this inconsistency between implicit and explicit representations may indicate separate underlying cognitive mechanisms, factors such as task-specific constraints and strategic variability must also be considered.

The Ventura Story

Ventura Publisher was the first desktop publishing software package to run on IBM PC compatible computers. Developed in the mid-1980s, Ventura was also the first desktop publishing application to incorporate features such as style sheets and automatic page layouts, allowing for long document formatting. This paper provides an autobiographical sketch of Lee Lorenzen, one of the founders of Ventura Software and developers of Ventura Publisher. Lorenzen outlines his early career in software and the founding story of Ventura Software and their innovative application. He also describes the early competitive landscape in desktop publishing software, including Aldus PageMaker, and then contrasts it with the key long document publishing features of Ventura Publisher such as style sheets, fast hyphenation and justification, automated layout algorithms, and database publishing.

JViz.RNA 4.0-Visualizing pseudoknots and RNA editing employing compressed tree graphs.

Previously, we have introduced an improved version of jViz.RNA which enabled faster and more stable RNA visualization by employing compressed tree graphs. However, the new RNA representation and visualization method required a sophisticated mechanism of pseudoknot visualization. In this work, we present our novel pseudoknot classification and implementation of pseudoknot visualization in the context of the new RNA graph model. We then compare our approach with other RNA visualization software, and demonstrate jViz.RNA 4.0’s benefits compared to other software. Additionally, we introduce interactive editing functionality into jViz.RNA and demonstrate its benefits in exploring and building RNA structures. The results presented highlight the new high degree of utility jViz.RNA 4.0 now offers. Users are now able to visualize pseudoknotted RNA, manipulate the resulting automatic layouts to suit their individual needs, and change both positioning and connectivity of the RNA molecules examined. Care was taken to limit overlap between structural elements, particularly in the case of pseudoknots to ensure an intuitive and informative layout of the final RNA structure.Availability: The software is freely available at: https://jviz.cs.sfu.ca/.

IStoryline: Effective Convergence to Hand-drawn Storylines.

Storyline visualization techniques have progressed significantly to generate illustrations of complex stories automatically. However, the visual layouts of storylines are not enhanced accordingly despite the improvement in the performance and extension of its application area. Existing methods attempt to achieve several shared optimization goals, such as reducing empty space and minimizing line crossings and wiggles. However, these goals do not always produce optimal results when compared to hand-drawn storylines. We conducted a preliminary study to learn how users translate a narrative into a hand-drawn storyline and check whether the visual elements in hand-drawn illustrations can be mapped back to appropriate narrative contexts. We also compared the hand-drawn storylines with storylines generated by the state-of-the-art methods and found they have significant differences. Our findings led to a design space that summarizes 1) how artists utilize narrative elements and 2) the sequence of actions artists follow to portray expressive and attractive storylines. We developed iStoryline, an authoring tool for integrating high-level user interactions into optimization algorithms and achieving a balance between hand-drawn storylines and automatic layouts. iStoryline allows users to create novel storyline visualizations easily according to their preferences by modifying the automatically generated layouts. The effectiveness and usability of iStoryline are studied with qualitative evaluations.

A Comparison of User-Generated and Automatic Graph Layouts

The research presented in this paper compares user-generated and automatic graph layouts. Following the methods suggested by van Ham et al. (2008), a group of users generated graph layouts using both multi-touch interaction on a tabletop display and mouse interaction on a desktop computer. Users were asked to optimize their layout for aesthetics and analytical tasks with a social network. We discuss characteristics of the user-generated layouts and interaction methods employed by users in this process. We then report on a web-based study to compare these layouts with the output of popular automatic layout algorithms. Our results demonstrate that the best of the user-generated layouts performed as well as or better than the physics-based layout. Orthogonal and circular automatic layouts were found to be considerably less effective than either the physics-based layout or the best of the user-generated layouts. We highlight several attributes of the various layouts that led to high accuracy and improved task completion time, as well as aspects in which traditional automatic layout methods were unsuccessful for our tasks.

An efficient grid layout algorithm for biological networks utilizing various biological attributes

BackgroundClearly visualized biopathways provide a great help in understanding biological systems. However, manual drawing of large-scale biopathways is time consuming. We proposed a grid layout algorithm that can handle gene-regulatory networks and signal transduction pathways by considering edge-edge crossing, node-edge crossing, distance measure between nodes, and subcellular localization information from Gene Ontology. Consequently, the layout algorithm succeeded in drastically reducing these crossings in the apoptosis model. However, for larger-scale networks, we encountered three problems: (i) the initial layout is often very far from any local optimum because nodes are initially placed at random, (ii) from a biological viewpoint, human layouts still exceed automatic layouts in understanding because except subcellular localization, it does not fully utilize biological information of pathways, and (iii) it employs a local search strategy in which the neighborhood is obtained by moving one node at each step, and automatic layouts suggest that simultaneous movements of multiple nodes are necessary for better layouts, while such extension may face worsening the time complexity.ResultsWe propose a new grid layout algorithm. To address problem (i), we devised a new force-directed algorithm whose output is suitable as the initial layout. For (ii), we considered that an appropriate alignment of nodes having the same biological attribute is one of the most important factors of the comprehension, and we defined a new score function that gives an advantage to such configurations. For solving problem (iii), we developed a search strategy that considers swapping nodes as well as moving a node, while keeping the order of the time complexity. Though a naïve implementation increases by one order, the time complexity, we solved this difficulty by devising a method that caches differences between scores of a layout and its possible updates.ConclusionLayouts of the new grid layout algorithm are compared with that of the previous algorithm and human layout in an endothelial cell model, three times as large as the apoptosis model. The total cost of the result from the new grid layout algorithm is similar to that of the human layout. In addition, its convergence time is drastically reduced (40% reduction).

Software visualization in software maintenance, reverse engineering, and re‐engineering: a research survey

AbstractSoftware visualization is concerned with the static visualization as well as the animation of software artifacts, such as source code, executable programs, and the data they manipulate, and their attributes, such as size, complexity, or dependencies. Software visualization techniques are widely used in the areas of software maintenance, reverse engineering, and re‐engineering, where typically large amounts of complex data need to be understood and a high degree of interaction between software engineers and automatic analyses is required. This paper reports the results of a survey on the perspectives of 82 researchers in software maintenance, reverse engineering, and re‐engineering on software visualization. It describes to which degree the researchers are involved in software visualization themselves, what is visualized and how, whether animation is frequently used, whether the researchers believe animation is useful at all, which automatic graph layouts are used if at all, whether the layout algorithms have deficiencies, and—last but not least—where the medium‐term and long‐term research in software visualization should be directed. The results of this survey help to ascertain the current role of software visualization in software engineering from the perspective of researchers in these domains and give hints on future research avenues. Copyright © 2003 John Wiley & Sons, Ltd.

Eco Cyc: encyclopedia of Escherichia coli genes and metabolism.

The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactions into 129 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc has many references to the primary literature, and is a (qualitative) computational model of E. coli metabolism. EcoCyc is available at URL http://ecocyc. PangeaSystems.com/ecocyc/

EcoCyc: Encyclopedia of Escherichia coli genes and metabolism.

The encyclopedia of Escherichia coli genes and metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of E.coli. The database describes 3030 genes of E.coli , 695 enzymes encoded by a subset of these genes, 595 metabolic reactions that occur in E.coli, and the organization of these reactions into 123 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc can be thought of as an electronic review article because of its copious references to the primary literature, and as a (qualitative) computational model of E.coli metabolism. EcoCyc is available at URL http://ecocyc.PangeaSystems.com/ecocyc/

EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism.

The Encyclopedia of Genes and Metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of Escherichia coli. It describes 2970 genes of E.coli, 547 enzymes encoded by these genes, 702 metabolic reactions that occur in E.coli and the organization of these reactions into 107 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc spans the space from sequence to function to allow scientists to investigate an unusually broad range of questions. EcoCyc can be thought of as both an electronic review article because of its copious references to the primary literature, and as an in silicio model of E.coli metabolism that can be probed and analyzed through computational means.

EcoCyc: an encyclopedia of Escherichia coli genes and metabolism.

The encyclopedia of Escherichia coli genes and metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of E.coli. It describes 2034 genes, 306 enzymes encoded by these genes, 580 metabolic reactions that occur in E.coli and the organization of these reactions into 100 metabolic pathways. The EcoCyc graphical user interface allows query and exploration of the EcoCyc database using visualization tools such as genomic map browsers and automatic layouts of metabolic pathways. EcoCyc spans the space from sequence to function to allow investigation of an unusually broad range of questions. EcoCyc can be thought of as both an electronic review article, because of its copious references to the primary literature, and as an in silico model of E.coli that can be probed and analyzed through computational means.

Automatic Variable-Width Routing for VLSI

Some of the essentials for layout of complex VLSI circuits are hierarchical design based on macrocells of arbitrary size and shape, power nets with local varying width, signal nets with individual width and very compacted layouts which still have to guarantee all geometrical design rules. This paper is devoted to the problem of automatic routing with real geometries. VWROUT, a Variable Width Routing System is presented. This includes planar power net routing with variable width on a single layer, loose and final routing of signal nets with variable width on two layers (H-V routing), and layout compaction with design-rule verification. Though automatic routing systems have been developed successfully, the intention of this paper is to demonstrate that layout programs of today have not yet become perfect. A lot of effort in software development is necessary in order that automatic layouts can compared with manual designs.