A General Introduction To Graph Visualization Techniques.

Tarawaneh, Raga'ad M.; Keller, Patric; Ebert, Achim

doi:10.4230/oasics.vluds.2011.151

Cited by 5 publications

(7 citation statements)

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“…Unlike other types of data visualization, in the node-link graphs, nodes' positions have no intrinsic meaning and are completely determined by convenience and readability. The layout with qualified readability should have the following characteristics: uniform distribution of nodes and edges, minimized edge-crossings, minimized edge bending ratio, minimized edge lengths, and so forth [TKE12]. Several node-link graphs' layout algorithms will be introduced here, however, they all fail to generate pathway maps.…”

Section: Introductionmentioning

confidence: 99%

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Automatically layout and visualize the biological pathway map with spectral graph theory

Xiao¹,

Wang²,

Li³

et al. 2022

Preprint

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The pathway is a biological term that refers to a series of interactions between molecules in a cell that cause a certain product or a change in the cell [NIH20]. Pathway analysis is a powerful method for gene expression analysis [Cir17]. Through pathway maps, the lists of genes that are differently expressed across the given phenotypes are translated into various biological phenomena [Nguyen2019].Visualizing a pathway map manually is a common practice nowadays because of the limitations of existing solutions to draw complicated graphs (i.e. directed graphs, graph with edge crossings, etc).This project provides a solution to draw pathway maps automatically based on spectral graph theory and topological sort. Various methods are taken to enhance pathway maps' readability. Significant reductions in the number of edge crossings and the sum of adjacent nodes are achieved.

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Section: Introductionmentioning

confidence: 99%

“…Force-directed layout, which is also known as the spring layout algorithm, is among the most popular layout algorithms for node-link diagrams [TKE12]. Each node is assumed to possess both attraction forces and repulsive forces.…”

Section: Introductionmentioning

confidence: 99%

Automatically layout and visualize the biological pathway map with spectral graph theory

Xiao¹,

Wang²,

Li³

et al. 2022

Preprint

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“…and the set of edges, which is the two-element subset of the set of nodes [40]. Graphs are applicable to present a lot of things in the everyday life and scientific research: the bus and subway systems with all their lines and stops, the association among people at work or in social media, the interaction of binding elements inside the cell like DNA segments, RNAs, proteins and smaller molecules.…”

Section: Graph Drawingmentioning

confidence: 99%

“…Graph drawing is a set of mathematical and computer science methods to generate visualizations of graphs [40]. This visualization often depicts the nodes and edges in the graph in node-link diagram (Figure 6) where nodes are presented with dots, circles, boxes, etc.…”

Section: Graph Drawingmentioning

confidence: 99%

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SubtiWiki 3.0: A relational database for the functional genome annotation of the model organism Bacillus subtilis

Zhu¹

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Biological databases emerged in the 1970s along with the rapid development of information science. Since then, they have greatly helped the research community in data management and information sharing, especially the model organism databases. Model organism databases focus on functional annotations of single well-studied model organisms, such as baker's yeast, Escherichia coli and Bacillus subtilis. B. subtilis is a model organism for Grampositive bacteria. It is of great importance in both labs and the industry and SubtiWiki is the model organism database dedicated to it. SubtiWiki is based on MediaWiki software and encourages the community to actively participate in the functional annotation of B. subtilis. With almost 9 years of constant updating, SubtiWiki has reached a state where the data it holds has outgrown the capacity of its engine. The limitations of the MediaWiki software have caused issues in data management, such as data duplication and inconsistency. Therefore, we have decided to migrate the SubtiWiki from MediaWiki to a relational database. The new database layout is structured, integrated and flexible as well. We included JavaScript Object Notation format to handle the challenges brought by the data complexity. In addition, batch operations of the data are now possible. Based on this new database layout, we built a content management system. With this system, the data of SubtiWiki can still be freely edited by the users and each edit is documented. With all data for protein-protein interaction and gene regulation cleaned from the wiki text, the visualization of large biological networks in B. subtilis is possible. Hence, we have included two more Subti-Apps, i.e. the interaction browser and the regulation browser. Those network browsers present biological networks at different levels. In addition, we introduced the genome browser for the access of DNA and protein sequences. The new implementation of SubtiWiki is user-and developer-friendly. Interactive data visualizations based on web technologies are created for efficient information communication. The modularized design makes SubtiWiki easily extendable. With the new database layout and Subti-Apps, SubtiWiki will continue serving the Bacillus research community by providing up-to-date and well-presented functional annotations of B. subtilis. 2 Introduction Biological databases are computer-based information systems for reliable storage and fast access of biological information. They emerged along with the rapid development of information science in the 1970s. The very first computer-based biological database "Protein Data Bank (PDB)" was initiated in the year 1971 [1]. In the same year, E. F. Codd proposed the relation theory for relational databases [2]. In 1982, the United States National Institute of Health (NIH) initiated the GenBank [3] project and simultaneously the European Molecular Biology Laboratory (EMBL) started its own sequence collection. In the middle of the 1980s, NIH and EMBL started the collaboration on data sharing and sync...

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