A layout algorithm for signaling pathways

Cataloged from PDF version of article.Visualization is crucial to the effective analysis of biological pathways. A poorly laid out pathway confuses the user, while a well laid out one improves the user's comprehension of the underlying biological phenomenon. We present a new, elegant algorithm for layout of biological signaling pathways. Our algorithm uses a force-directed layout scheme, taking into account directional and rectangular regional constraints enforced by different molecular interaction types and subcellular locations in a cell. The algorithm has been successfully implemented as part of a pathway visualization and analysis toolkit named PATIKA, and results with respect to computational complexity and quality of the layout have been found satisfactory. The algorithm may be easily adapted to be used in other applications with similar conventions and constraints as well. PATIKA version 1.0 beta is available upon request at http://www.patika.org. (C) 2004 Elsevier Inc. All rights reserved

Combinatorial pattern matching

Cataloged from PDF version of article.15th Annual Symposium, CPM 2004 : Istambul, Turkey, July 5-7, 2004 : proceeding

Electrocardiographic Imaging of Sinus Rhythm in Pig Hearts Using Bayesian Maximum A Posteriori Estimation

Background: Electrocardiographic imaging (ECGI) has potential to guide physicians to plan treatment strategies. Previously, Bayesian maximum a posteriori (MAP) estimation has been successfully applied to solve this inverse problem for paced data. In this study, we evaluate its effectiveness using experimental data in reconstructing sinus rhythm. Methods: Four datasets from Langendorff-perfused pig hearts, suspended in a human-shaped torso-tank, were used. Each experiment included 3-5 simultaneous electrogram (EGM) and body surface potential (BSP) recordings of 10 beats, in baseline and under dofetilide and pinacidil perfusion. Bayesian MAP estimation and Tikhonov regularization were used to solve the inverse problem. Prior models in MAP were generated using beats from the same recording but excluding the test beat. Pearson's correlation was used to evaluate EGM reconstructions, activation time (AT) maps, and gradient of ATs. Results: In almost all quantitative evaluations and qualitative comparisons of AT maps and epicardial breakthrough sites, MAP outperformed substantially better than Tikhonov regularization. Conclusion: These preliminary results showed that with a "good" prior model, MAP improves over Tikhonov regularization in terms of preventing misdiagnosis of conduction abnormalities associated with arrhythmogenic substrates and identifying epicardial breakthrough sites

Algorithms for Layout of Disconnected Graphs

We present efficient algorithms for the layout of disconnected objects in a graph (isolated nodes and components) for a specified aspect ratio. These linear and near-linear algorithms are based on alternate-bisection and two-dimensional packing methodologies. In addition, the parameters that affect the performance of these algorithms as well as the circumstances under which the two methodologies perform well are analyzed

A layout algorithm for undirected compound graphs

Cataloged from PDF version of article.We present an algorithm for the layout of undirected compound graphs, relaxing restrictions of previously known algorithms in regards to topology and geometry. The algorithm is based on the traditional force-directed layout scheme with extensions to handle multi-level nesting, edges between nodes of arbitrary nesting levels, varying node sizes, and other possible application-specific constraints. Experimental results show that the execution time and quality of the produced drawings with respect to commonly accepted layout criteria are quite satisfactory. The algorithm has also been successfully implemented as part of a pathway integration and analysis toolkit named PATIKA, for drawing complicated biological pathways with compartmental constraints and arbitrary nesting relations to represent molecular complexes and various types of pathway abstractions. (C) 2008 Elsevier Inc. All rights reserved

On labeling in graph visualization

Cataloged from PDF version of article.When visualizing graphs, it is essential to communicate the meaning of each graph object via text or graphical labels. Automatic placement of labels in a graph is an NP-Hard problem, for which efficient heuristic solutions have been recently developed. In this paper, we describe a general framework for modeling, drawing, editing, and automatic placement of labels respecting user constraints. In addition, we present the interface and the basic engine of the Graph Editor Toolkit – a family of portable graph visualization libraries designed for integration into graphical user interface application programs. This toolkit produces a high quality automated placement of labels in a graph using our framework. A brief survey of automatic label placement algorithms is also presented. Finally we describe extensions to certain existing automatic label placement algorithms, allowing their integration into this visualization tool. (C) 2007 Elsevier Inc. All rights reserved

VISIBIOweb: visualization and layout services for BioPAX pathway models

With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, web-based pathway visualization and layout service for pathway models in BioPAX format. With VISIBIOweb, one can obtain well-laid-out views of pathway models using the standard notation of the Systems Biology Graphical Notation (SBGN), and can embed such views within one's web pages as desired. Pathway views may be navigated using zoom and scroll tools; pathway object properties, including any external database references available in the data, may be inspected interactively. The automatic layout component of VISIBIOweb may also be accessed programmatically from other tools using Hypertext Transfer Protocol (HTTP). The web site is free and open to all users and there is no login requirement. It is available at: http://visibioweb.patika.org