Reactome diagram viewer: data structures and strategies to boost performance.
Reactome diagram viewer: data structures and strategies to boost performance.
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DOI：
10.1093/bioinformatics/btx752
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发表时间：
2018-04-01
期刊：
影响因子：
--
通讯作者：
Hermjakob H
中科院分区：
文献类型：
--
作者：
Fabregat A;Sidiropoulos K;Viteri G;Marin-Garcia P;Ping P;Stein L;D'Eustachio P;Hermjakob H
Reactome是一个免费，开源，开放数据，策划和同行评审的生物分子途径知识库。对于基于网络的途径可视化，Reactome使用了一个自定义的途径图查看器，该查看器在过去几年中已经发展成熟。在这里，我们根据广泛的可用性测试会议和技术开发，提出了全面的可用性和性能增强，旨在优化查看器，以满足社区的需求。路径图查看器版本3实现了持续更好的性能，在不到1秒的时间内加载和渲染Reactome中97%的图表。将多层html5 canvas策略与空间分区数据结构相结合，最大限度地减少了CPU工作负载，从而引入了进一步增强用户体验的新功能。通过使用高度优化的数据结构和算法，Reactome提高了新的路径图查看器的性能和可用性，为路径可视化提供了一个强大，可扩展和易于集成的解决方案。由于复杂数据的基于图形的可视化是生物信息学中的一个常见挑战，因此本文提出的许多策略适用于各种基于Web的生物信息学资源。Reactome可在线访问：https://reactome.org。图表查看器是Reactome路径浏览器（https：//reactome.org/PathwayBrowser/）的一部分，也可作为独立的小部件访问：https://reactome.org/dev/diagram/。源代码可以在https://github.com/reactome-pwp/diagram上免费获得。 补充数据可在Bioinformatics在线获得。
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. The pathway diagram viewer version 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. 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: https://reactome.org/dev/diagram/. The source code is freely available at: https://github.com/reactome-pwp/diagram. Supplementary data are available at Bioinformatics online.
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影响因子：
14.9
作者：
Kutmon M;Riutta A;Nunes N;Hanspers K;Willighagen EL;Bohler A;Mélius J;Waagmeester A;Sinha SR;Miller R;Coort SL;Cirillo E;Smeets B;Evelo CT;Pico AR
通讯作者：
Pico AR
影响因子：
4
作者：
Gawron, Piotr;Ostaszewski, Marek;Schneider, Reinhard
通讯作者：
Schneider, Reinhard
DOI：
10.1145/130844.130856
发表时间：
1992-06-01
期刊：
COMPUTING SURVEYS
影响因子：
--
作者：
KRUEGER, CW
通讯作者：
KRUEGER, CW
影响因子：
14.9
作者：
Cerami EG;Gross BE;Demir E;Rodchenkov I;Babur O;Anwar N;Schultz N;Bader GD;Sander C
通讯作者：
Sander C
影响因子：
46.9
作者：
Le Novere, Nicolas;Hucka, Michael;Kitano, Hiroaki
通讯作者：
Kitano, Hiroaki