Browsing by Subject "Software system"

Now showing 1 - 3 of 3

Open Access
Chisio : a visual framework for compound graph editing and layout
(2007) Küçükkeçeci, Cihan
Graphs are data models, widely used in many areas from networking to biology to computer science. Visualization, interactive editing ability and layout of graphs are critical issues when analyzing the underlying relational information. There are many commercial and non-commercial graph visualization tools. However, overall support for compound or hierarchically organized graph representations is very limited. We introduce a new open-source editing and layout framework named Chisio for compound graphs. Chisio is developed as a free, easy-to-use and powerful academic graph visualization tool, supporting various automatic layout algorithms. It is written in Java and based on Eclipse’s Graphical Editing Framework (GEF). Chisio can be used as a finished generic compound graph editor with standard graph editing facilities such as zoom, scroll, add or remove graph objects, move, and resize. Object property and layout options dialogs are provided to modify existing graph object properties and layout options, respectively. In addition, printing or saving the current drawing as a static image and persistent storage facilities are supported. Saved graphs or GraphML formatted files created by other tools can be loaded into Chisio. Furthermore, a highlight mechanism is provided to emphasize subgraphs of users interest. The framework has an architecture suitable for easy customization of the tool for end-users’ specific needs as well. Also Chisio offers several layout styles from the basic spring embedder to hierarchical layout to compound spring embedder to circular layout. Furthermore, new algorithms are straightforward to add, making Chisio an ideal test environment for layout algorithm developers.
Open Access
VISIBIOweb : a web-based visualization and layout service for biological pathways
(2009) Dilek, Alptuğ
A biological pathway is a representation of biological reactions between molecules in a living cell. At present, there are hundreds of Internet-accessible databases storing biological pathway data. Exchanging, handling, and storing this data are crucial in terms of both providing understandability and allowing further enhancements on the gathered data. As a result of this necessity, many biological models were developed to cluster the data in a meaningful manner under a semantically reasonable hierarchy. As the amount and complexity of the data increases, visualization of pathways becomes inevitable. Graphs are inherently suitable for modeling pathways. The task of creating a visual representation for pathways dynamically requires methods from the area of graph visualization. As a result, many software systems, which can interpret the pathway data with a graph structure and visualize the constructed graph, emerged. However, many of these software systems are insufficient due to poor complexity handling of the underlying model, lack of visual standardization or long installation steps. In this thesis, we introduce VISIBIOweb, a new open-source and web-based visualization service for biological pathway models stored in BioPAX (Biological Pathways Exchange Language) format. VISIBIOweb runs on Apache Tomcat server and is implemented in Java based on Eclipse GEF (Graphical Editing Framework). Google Maps API is used on the client side as the core component to visualize the representation constructed on the server. VISIBIOweb supports basic graph viewing functionalities such as zooming, scrolling, and selection of graph objects. The inspector window is provided to view the properties of the selected graph object. Once the view for the uploaded biological model is created, it can be stored as a static image. The biological models can also be persisted and embedded within other web sites just like Google Maps. The layout information of the constructed graph is also provided in an XML-based format. The introduction of such a format is a good starting point to develop an official layout extension for BioPAX format.
Open Access
Visuall: a quickly customizable library for jumpstarting visual graph analysis components
(2021-09) Canbaz, Yusuf Sait
Graph visualization is an area of information visualization, where relational data is depicted in the form of nodes (objects) and edges (links). Many people or organizations utilize graph visualization for insightful analysis and interpretation of relational data. In graph visualization, primary challenges include complexity management, eﬃcient database querying, and customization for speciﬁc domains. Visuall aims to solve these problems by providing a generic, highly customizable, and easily conﬁgurable software component for building web-based visual graph analysis tools. Essential functionalities needed by such visual analysis components include manually or automatically setting the layout of graph elements, support for nested or hierarchical drawings, eﬃcient querying of the database or client-side data, emphasizing or highlighting graph elements of interest, customization of visuals and styles, clustering, calculating graph-theoretical properties, and time-based ﬁltering of graph elements. Although Visuall provides all these functionalities out of the box for jumpstarting, customization of software for domain-speciﬁc needs is still unavoidable. Such software changes might result in complications due to unstructured code and code ignoring the invariants assumed by the orig-inal development team. To prevent these and to facilitate easily maintainable customization, Visuall provides a modular architecture. Furthermore, the devel-opers straightforwardly upgrade the software so long as the Visuall developers and the users developing visual analysis components based on Visuall maintain the provided architecture. We tested our database queries on a database that contains about half a million graph elements. We also examined our client-side operations up to a thousand graph elements. In both client-side and database operations, we observe that operations take at most several seconds, making Visuall convenient for interactive exploration and analysis of networks.