Reactome diagram viewer: data structures and strategies to boost performance

Antonio Fabregat, Konstantinos Sidiropoulos, Guilherme Viteri, Pablo Marin-Garcia, Peipei Ping, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob, Janet Kelso
2017 Bioinformatics  
Motivation: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimize the viewer towards the needs of the community. Results: The pathway diagram viewer
more » ... rsion 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s. Combining the multi-layer html5 canvas strategy with a space partitioning data structure minimizes CPU workload, enabling the introduction of new features that further enhance user experience. Through the use of highly optimized data structures and algorithms, Reactome has boosted the performance and usability of the new pathway diagram viewer, providing a robust, scalable and easy-to-integrate solution to pathway visualization. As graph-based visualization of complex data is a frequent challenge in bioinformatics, many of the individual strategies presented here are applicable to a wide range of web-based bioinformatics resources. Availability and implementation: Reactome is available online at: https://reactome.org. The diagram viewer is part of the Reactome pathway browser (https://reactome.org/PathwayBrowser/) and also available as a stand-alone widget at:
doi:10.1093/bioinformatics/btx752 pmid:29186351 pmcid:PMC6030826 fatcat:j4wrfd3v7fcwjb2ykhitis3apa