BioVisReport: A Markdown-based lightweight website builder for reproducible and interactive visualization of results from peer-reviewed publications
Interactive visualization is an effective way to promote the reproducibility of results presented in biomedical publications and to facilitate additional exploration of the reported data. However, there is a lack of convenient tools that balance reproducibility with ease of use. To address this prob...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022002240 |
| _version_ | 1828087942522863616 |
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| author | Jingcheng Yang Yaqing Liu Jun Shang Yechao Huang Ying Yu Zhihui Li Leming Shi Zihan Ran |
| author_facet | Jingcheng Yang Yaqing Liu Jun Shang Yechao Huang Ying Yu Zhihui Li Leming Shi Zihan Ran |
| author_sort | Jingcheng Yang |
| collection | DOAJ |
| description | Interactive visualization is an effective way to promote the reproducibility of results presented in biomedical publications and to facilitate additional exploration of the reported data. However, there is a lack of convenient tools that balance reproducibility with ease of use. To address this problem, we develop BioVisReport, a lightweight solution for the rapid generation of an interactive website based on a user-defined Markdown file, which acts as a text markup language without requiring users to master complex syntax and allows them to preview the results in real-time. Interactive websites generated by the tool can help readers conveniently reproduce research findings and perform further in-depth analyses beyond those reported in the original peer-reviewed publications. Currently, BioVisReport offers 17 basic types of plots for visualizing published data. In addition, the extensibility of BioVisReport supports flexible integration of user-developed Python plugins with multiple programming languages. BioVisReport is freely available at https://biovis.report/. |
| first_indexed | 2024-04-11T05:19:09Z |
| format | Article |
| id | doaj.art-14e20af5bef64939aaa6711a7e7398d4 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:19:09Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-14e20af5bef64939aaa6711a7e7398d42022-12-24T04:52:53ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012031333139BioVisReport: A Markdown-based lightweight website builder for reproducible and interactive visualization of results from peer-reviewed publicationsJingcheng Yang0Yaqing Liu1Jun Shang2Yechao Huang3Ying Yu4Zhihui Li5Leming Shi6Zihan Ran7State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, 2005 Songhu Road, Shanghai 200438, China; Greater Bay Area Institute of Precision Medicine, 115 Jiaoxi Road, Guangzhou 511458, ChinaState Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, 2005 Songhu Road, Shanghai 200438, ChinaState Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, 2005 Songhu Road, Shanghai 200438, ChinaState Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, 2005 Songhu Road, Shanghai 200438, ChinaState Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, 2005 Songhu Road, Shanghai 200438, ChinaState Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, 2005 Songhu Road, Shanghai 200438, ChinaState Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, 2005 Songhu Road, Shanghai 200438, ChinaDepartment of Research, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, 1500 Zhouyuan Road, Shanghai 201318, China; Inspection and Quarantine Department, The College of Medical Technology, Shanghai University of Medicine & Health Sciences, 279 Zhouzhu Road, Shanghai 201318, China; Corresponding author at: Department of Research, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, 1500 Zhouyuan Road, Shanghai 201318, China.Interactive visualization is an effective way to promote the reproducibility of results presented in biomedical publications and to facilitate additional exploration of the reported data. However, there is a lack of convenient tools that balance reproducibility with ease of use. To address this problem, we develop BioVisReport, a lightweight solution for the rapid generation of an interactive website based on a user-defined Markdown file, which acts as a text markup language without requiring users to master complex syntax and allows them to preview the results in real-time. Interactive websites generated by the tool can help readers conveniently reproduce research findings and perform further in-depth analyses beyond those reported in the original peer-reviewed publications. Currently, BioVisReport offers 17 basic types of plots for visualizing published data. In addition, the extensibility of BioVisReport supports flexible integration of user-developed Python plugins with multiple programming languages. BioVisReport is freely available at https://biovis.report/.http://www.sciencedirect.com/science/article/pii/S2001037022002240ReproducibilityWebsite builderInteractive visualizationPeer-reviewed publications |
| spellingShingle | Jingcheng Yang Yaqing Liu Jun Shang Yechao Huang Ying Yu Zhihui Li Leming Shi Zihan Ran BioVisReport: A Markdown-based lightweight website builder for reproducible and interactive visualization of results from peer-reviewed publications Computational and Structural Biotechnology Journal Reproducibility Website builder Interactive visualization Peer-reviewed publications |
| title | BioVisReport: A Markdown-based lightweight website builder for reproducible and interactive visualization of results from peer-reviewed publications |
| title_full | BioVisReport: A Markdown-based lightweight website builder for reproducible and interactive visualization of results from peer-reviewed publications |
| title_fullStr | BioVisReport: A Markdown-based lightweight website builder for reproducible and interactive visualization of results from peer-reviewed publications |
| title_full_unstemmed | BioVisReport: A Markdown-based lightweight website builder for reproducible and interactive visualization of results from peer-reviewed publications |
| title_short | BioVisReport: A Markdown-based lightweight website builder for reproducible and interactive visualization of results from peer-reviewed publications |
| title_sort | biovisreport a markdown based lightweight website builder for reproducible and interactive visualization of results from peer reviewed publications |
| topic | Reproducibility Website builder Interactive visualization Peer-reviewed publications |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022002240 |
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