A New Constraint-Based Compound Graph Layout Algorithm for Drawing Biochemical Networks

2011 ◽  
pp. 407-424
Author(s):  
Sabri Skhiri dit Gabouje ◽  
Esteban Zimányi
Keyword(s):  
Genetic Regulation ◽  
Biochemical Networks ◽  
Visualization Tool ◽  
Graph Layout ◽  
Layout Algorithm ◽  
Data Semantics ◽  
Visualization Tools ◽  
Generic Representation ◽  
Compound Graph ◽  
Single Graph

Due to the huge amount of information available in biochemical databases, biologists need sophisticated tools to accurately extract the information from such databases and to interpret it correctly. Those tools must be able to dynamically generate any kind of biochemical subgraph (i.e., metabolic pathways, genetic regulation, signal transduction, etc.) in a single graph. The visualization tools must be able to cope with such graphs and to take into account the particular semantics of all kinds of biochemical subgraphs. Therefore, such tools need generic graph layout algorithms that adapt their behavior to the data semantics. In this paper we present the Constrained Compound Graph Layout (C2GL) algorithm designed for the generic representation of biochemical graphs and in which users can represent knowledge about how to draw graphs in accordance with the biochemical semantics. We show how we implemented the C2GL algorithm in the Visual BioMaze framework, the visualization tool of the BioMaze project.

scholarly journals A Compound Graph Layout Algorithm for Biological Pathways

2005 ◽  
pp. 442-447 ◽  
Author(s):  
Ugur Dogrusoz ◽  
Erhan Giral ◽  
Ahmet Cetintas ◽  
Ali Civril ◽  
Emek Demir
Keyword(s):  
Biological Pathways ◽  
Graph Layout ◽  
Layout Algorithm ◽  
Compound Graph

The Application of Lightweight Visualization Tool-Product View to Aircraft Development

2013 ◽  
Vol 376 ◽  
pp. 307-311
Author(s):  
Hai Jun Yin ◽  
Ye Hu
Keyword(s):  
High Performance ◽  
Comprehensive Evaluation ◽  
Model Simulation ◽  
Design And Technology ◽  
Visualization Tool ◽  
Communication Tool ◽  
Application Process ◽  
Collaborative Communication ◽  
Digital Products ◽  
Visualization Tools

This article describes the function of lightweight visualization tool--Product View. It introduces the application process of lightweight visualization tool--Product View in aircraft development from lightweight model assembly, lightweight model simulation, visual collaboration, collaboration between R & D, and human factor analysis, etc. Product View is a better collaborative communication tool between process design and design, design and technology in the aircraft development.There are not only high demands on the design and assembly, but also a lot of cooperative work between different equipments, equipments and staff, different staff in aircraft development[1]. In order to more efficiently share and use the digital product content created in this process, the demands on high-performance lightweight visualization tool become more and more strongly. Compatibility[2] and interactivity[3] are the two most important indicators when choosing a lightweight visualization tool. Variety of different tools may be used to create digital products during the design process, the compatibility between lightweight visualization tools and digital tools helps to enhance the user’s experience. The interactivity of lightweight visualization tools is also indispensable, it can timely discover the problems of geometric dimensions, tolerance annotations, elements conflict, and interference, give a comprehensive evaluation of the design, and then provide an effective medium between engineering, manufacturing and other downstream participants.

Building Network Visualization Tools to Facilitate Metacognition in Complex Analysis

Leonardo ◽  
2011 ◽  
Vol 44 (3) ◽  
pp. 248-249
Author(s):  
Barbara Mirel
Keyword(s):  
Complex Analysis ◽  
Tool Design ◽  
Network Visualization ◽  
Visualization Tool ◽  
Complex Tasks ◽  
Interactive Network ◽  
Visualization Tools

If whole communities of domain analysts are to be able to use interactive network visualization tools productively and efficiently, tool design needs to adequately support the metacognition implicit in complex visual analytic tasks. Metacognition for such exploratory network-mediated tasks applies across disciplines. This essay presents metacognitive demands inherent in complex tasks aimed at uncovering relevant relationships for hypothesizing purposes and proposes network visualization tool designs that can support these metacognitive demands.

The Efficacy of a Low-Level Program Visualization Tool for Teaching Programming Concepts to Novice C Programmers

2000 ◽  
Vol 22 (2) ◽  
pp. 187-215 ◽  
Author(s):  
Philip A. Smith ◽  
Geoffrey I. Webb
Keyword(s):  
Empirical Evidence ◽  
Experimental Confirmation ◽  
Program Execution ◽  
Visualization Tool ◽  
Program Visualization ◽  
Low Level ◽  
The Past ◽  
New Concepts ◽  
Visualization Tools

It is widely agreed that learning to program is difficult. Program visualization tools make visible aspects of program execution which are often hidden from the user. While several program visualization tools aimed at novice programmers have been developed over the past decade there is little empirical evidence showing that novices actually benefit from their use [1]. In this article we describe a “Glass-box Interpreter” called Bradman. An experiment is presented which tests the efficacy of Bradman in assisting novice programmers learn programming concepts. We show that students that used the glass-box interpreter achieved greater understanding of some programming concepts than those without access. We also give evidence that the student's ability to assimilate new concepts was enhanced by exposure to the glass-box interpreter. This is experimental confirmation that such tools are beneficial in helping novices learn programming.

scholarly journals Using NViz tool for Environmental Sensor Networks

1970 ◽  
Vol 7 (1) ◽  
pp. 52-58
Author(s):  
Anh-Vu Dinh-Duc
Keyword(s):  
Sensor Networks ◽  
Development Process ◽  
Wireless Sensor ◽  
Visualization Tool ◽  
Layered Architecture ◽  
Environmental Sensor Networks ◽  
The Status ◽  
Speed Up ◽  
Environmental Sensor ◽  
Visualization Tools

Visualization tools help users to observe the status of the Wireless Sensor Networks (WSNs). Although various visualization tools have been created for certain projects so far, these tools can only be used in certain scenarios, due to their hard-coded packet formats and network’s properties. To speed up development process, a visualization tool which can adapt to any kind of WSN is essentially necessary. A generalpurpose visualization tool - NViz, which can represent and visualize data for all WSN applications, is proposed. NViz allows user to set their network’s properties and packet formats through XML files. Based on properties defined, user can choose the meaning of them and let NViz represents the data respectively. Furthermore, a better Replay mechanism, which lets researchers and developers debug their WSN easily, is also integrated in this tool. NViz is designed based on a layered architecture which allows for clear and well-defined interrelationships and interfaces between each components. As a demonstration, NViz is used for designing an environmental sensor network.

scholarly journals Gragnostics: Fast, Interpretable Features for Comparing Graphs

2019 ◽  
Author(s):  
Robert Gove
Keyword(s):  
Machine Learning ◽  
Social Network ◽  
Social Network Analysis ◽  
Network Analysis ◽  
Linear Time ◽  
Interactive Visualization ◽  
Visualization Tool ◽  
Graph Visualization ◽  
Learning Classifier ◽  
Visualization Tools

Many analytical tasks, such as social network analysis, depend on comparing graphs. Existing methods are slow, or can be difficult to understand. To address these challenges, this paper proposes gragnostics, a set of 10 fast, layperson-understandable graph-level features. Each can be computed in linear time. To evaluate the ability of these features to discriminate different topologies and types of graphs, this paper compares a machine learning classifier using gragnostics to alternative classifiers, and the evaluation finds that the gragnostics classifier achieves higher performance. To evaluate gragnostics' utility in interactive visualization tools, this paper presents Chiron, a graph visualization tool that enables users to explore the subgraphs of a larger graph. Example usage scenarios of Chiron demonstrate that using gragnostics in a rank-by-feature framework can be effective for finding interesting subgraphs.

Exploring the Spread of Zika

2019 ◽  
pp. 678-702
Author(s):  
Oluwakemi Ola ◽  
Olha Buchel ◽  
Kamran Sedig
Keyword(s):  
Public Health ◽  
Economic Growth ◽  
Adverse Impact ◽  
Visualization Tool ◽  
Human Environment ◽  
Vector Borne Diseases ◽  
Public Health Threat ◽  
Interactive Visualizations ◽  
Vector Borne ◽  
Visualization Tools

Vector-borne diseases pose a major public health threat. Combined, these diseases contribute significantly to illness and mortality worldwide and have an adverse impact on development and economic growth of nations. Public health stakeholders seeking to control and prevent these diseases are confronted with a myriad of challenges. Some of these difficulties are related to the nature of the data, the uncertainty of disease dynamics, and volatility of human-environment interactions. Visualization tools are capable of ameliorating some of these challenges. In this paper, the authors demonstrate how interactive visualizations can support stakeholders' decision-making tasks. In particular, they present a visualization tool they created that can support control efforts related to the recent Zika outbreak in Brazil.

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