The Research And Development Of Pathbubbles-an Interactive Visualization System For Biological Pathway Analysis

Due to the rapid advance in biological technique, lots of pathway data aregenerated. With the development of bioinformatics, a huge amount of biologicalexperimental data is accumulated. As we know, human can interpret visualinformation rapidly, it is vital to describe the data in a comprehensive and interactivevisualization manner. However, human has limited memory. Current visualizationtools just provide a way to navigate and manipulate the data, metal workload can notbe reduced. For example: most of data analysis process is various, which requiresmany different application windows to display different information processing result.In addition, although existing biological databases, such as Reactome and KEGG,provide an abundant of information, they lack a user-friendly and interactivevisualization analysis interface.In the views of those problems, we present PathBubbles, a web-basedinteractive biological pathway visualization system. A key aspect of PathBubbles isextending static multiple views to a metaphorical interface of Bubbles, each of whichis treated as a functional unit view. Bubbles do not overlap, they can be grouped andungrouped. This bubbles metaphor interaction interface will help users switch theviews quickly and conveniently and reduce their metal workload, which can helpbiologists to explore and interpret the underlying information of the pathways. Morespecific introductions are described as below.(1) Pathways visualization Bubble: In PathBubbles, pathway can be representedby a Node-link diagram, some compartment information is also be integrated. So wepresent a hybrid algorithm, which uses the combination of hierarchical pathwaylayout algorithm and force direct layout algorithm to arrange the pathway. Besides,an online pathway platform is also developed for biologists to edit and improvebiological pathway.(2) Sunburst visualization Bubbles: PathBubbles integrates all the existingpathways of Reactome in a single Sunburst, and uses color to map interestinginformation, which is convenient to compare, query and validate hypothesis.Sunburst can provide a global view in a first glance, detailed biomolecules of eachpathway can also be visualized as a child-Sunburst. The data selection and processingway is from global to local, which is consistent with biological data analysis progress. (3) Interactive Table visualization Bubble: Specific information of biologicalpathway are displayed in the form of a interactive table, which is the most familiarway for biologist to do data analysis.In a word, we focus on the research on following aspects: design of interactivevisualization system, automatic pathway diagram arrangement algorithm, and thevisualization design of pathway analysis. The dynamic interaction between multi-view datasets visualization improves the data analysis and exploration.