Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization

Author:

Li Jianfeng12ORCID,Miao Benben3ORCID,Wang Shixiang4ORCID,Dong Wei5,Xu Houshi6,Si Chenchen7,Wang Wei8,Duan Songqi9ORCID,Lou Jiacheng10,Bao Zhiwei11,Zeng Hailuan12,Yang Zengzeng13,Cheng Wenyan1,Zhao Fei1415,Zeng Jianming16,Liu Xue-Song4,Wu Renxie3ORCID,Shen Yang1,Chen Zhu1,Chen Saijuan1,Wang Mingjie17,

Affiliation:

1. Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine , Shanghai, China

2. School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai, China

3. College of Fisheries, Guangdong Ocean University , Zhanjiang, Guangdong, China

4. School of Life Science and Technology, ShanghaiTech University , Shanghai, China

5. Zhongshan School of Medicine, Sun Yat-sen University , Guangzhou, China

6. Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai, China

7. Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine , Shanghai, China

8. Department of Urology, First Hospital of Shanxi Medical University , Taiyuan, China

9. College of Food Science, Sichuan Agricultural University , Yaan, China

10. Department of Neurosurgery, The Second Affiliated Hospital of Dalian Medical University , Dalian, China

11. State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou, China

12. Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan Institute for Metabolic Diseases, and Human Phenome Institute, Fudan University , Shanghai, China

13. Qinghai Academy of Animal and Veterinary Science, State Key Laboratory of Plateau Ecology and Agriculture in the Three River Head Waters Region, Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland Qinghai University , Xining, China

14. National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai, China

15. University of the Chinese Academy of Sciences , Beijing, China

16. Faculty of Health Sciences, University of Macau , Taipa, Macau, China

17. Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine , Shanghai, China

Abstract

Abstract Complex biomedical data generated during clinical, omics and mechanism-based experiments have increasingly been exploited through cloud- and visualization-based data mining techniques. However, the scientific community still lacks an easy-to-use web service for the comprehensive visualization of biomedical data, particularly high-quality and publication-ready graphics that allow easy scaling and updatability according to user demands. Therefore, we propose a community-driven modern web service, Hiplot (https://hiplot.org), with concise and top-quality data visualization applications for the life sciences and biomedical fields. This web service permits users to conveniently and interactively complete a few specialized visualization tasks that previously could only be conducted by senior bioinformatics or biostatistics researchers. It covers most of the daily demands of biomedical researchers with its equipped 240+ biomedical data visualization functions, involving basic statistics, multi-omics, regression, clustering, dimensional reduction, meta-analysis, survival analysis, risk modelling, etc. Moreover, to improve the efficiency in use and development of plugins, we introduced some core advantages on the client-/server-side of the website, such as spreadsheet-based data importing, cross-platform command-line controller (Hctl), multi-user plumber workers, JavaScript Object Notation-based plugin system, easy data/parameters, results and errors reproduction and real-time updates mode. Meanwhile, using demo/real data sets and benchmark tests, we explored statistical parameters, cancer genomic landscapes, disease risk factors and the performance of website based on selected native plugins. The statistics of visits and user numbers could further reflect the potential impact of this web service on relevant fields. Thus, researchers devoted to life and data sciences would benefit from this emerging and free web service.

Funder

Shanghai Science and Technology Commission, Science and technology Innovation Action Plan Sailing Project

State Key Laboratory of Medical Genomics

Double First-Class Project

Ministry of Education

Publisher

Oxford University Press (OUP)

Subject

Molecular Biology,Information Systems

Reference34 articles.

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