SynBioTools: a one-stop facility for searching and selecting synthetic biology tools
Abstract Background The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry o...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-04-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-023-05281-5 |
| _version_ | 1797840808511012864 |
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| author | Pengli Cai Sheng Liu Dachuan Zhang Huadong Xing Mengying Han Dongliang Liu Linlin Gong Qian-Nan Hu |
| author_facet | Pengli Cai Sheng Liu Dachuan Zhang Huadong Xing Mengying Han Dongliang Liu Linlin Gong Qian-Nan Hu |
| author_sort | Pengli Cai |
| collection | DOAJ |
| description | Abstract Background The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology. Results We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools. SynBioTools includes databases, computational tools, and methods extracted from reviews via SCIentific Table Extraction, a scientific table-extraction tool that we built. Approximately 57% of the resources that we located and included in SynBioTools are not mentioned in bio.tools, the dominant tool registry. To improve users’ understanding of the tools and to enable them to make better choices, the tools are grouped into nine modules (each with subdivisions) based on their potential biosynthetic applications. Detailed comparisons of similar tools in every classification are included. The URLs, descriptions, source references, and the number of citations of the tools are also integrated into the system. Conclusions SynBioTools is freely available at https://synbiotools.lifesynther.com/ . It provides end-users and developers with a useful resource of categorized synthetic biology databases, tools, and methods to facilitate tool retrieval and selection. |
| first_indexed | 2024-04-09T16:20:43Z |
| format | Article |
| id | doaj.art-ae970e62b2744278a4dbfc1b880979f3 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-09T16:20:43Z |
| publishDate | 2023-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-ae970e62b2744278a4dbfc1b880979f32023-04-23T11:29:56ZengBMCBMC Bioinformatics1471-21052023-04-0124111110.1186/s12859-023-05281-5SynBioTools: a one-stop facility for searching and selecting synthetic biology toolsPengli Cai0Sheng Liu1Dachuan Zhang2Huadong Xing3Mengying Han4Dongliang Liu5Linlin Gong6Qian-Nan Hu7CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of SciencesCAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of SciencesEcological Systems Design, Institute of Environmental Engineering, ETH ZurichCAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of SciencesCAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of SciencesCAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of SciencesCAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of SciencesCAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of SciencesAbstract Background The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology. Results We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools. SynBioTools includes databases, computational tools, and methods extracted from reviews via SCIentific Table Extraction, a scientific table-extraction tool that we built. Approximately 57% of the resources that we located and included in SynBioTools are not mentioned in bio.tools, the dominant tool registry. To improve users’ understanding of the tools and to enable them to make better choices, the tools are grouped into nine modules (each with subdivisions) based on their potential biosynthetic applications. Detailed comparisons of similar tools in every classification are included. The URLs, descriptions, source references, and the number of citations of the tools are also integrated into the system. Conclusions SynBioTools is freely available at https://synbiotools.lifesynther.com/ . It provides end-users and developers with a useful resource of categorized synthetic biology databases, tools, and methods to facilitate tool retrieval and selection.https://doi.org/10.1186/s12859-023-05281-5Synthetic biologyComputational toolDatabaseTool retrievalTool registryTable extraction |
| spellingShingle | Pengli Cai Sheng Liu Dachuan Zhang Huadong Xing Mengying Han Dongliang Liu Linlin Gong Qian-Nan Hu SynBioTools: a one-stop facility for searching and selecting synthetic biology tools BMC Bioinformatics Synthetic biology Computational tool Database Tool retrieval Tool registry Table extraction |
| title | SynBioTools: a one-stop facility for searching and selecting synthetic biology tools |
| title_full | SynBioTools: a one-stop facility for searching and selecting synthetic biology tools |
| title_fullStr | SynBioTools: a one-stop facility for searching and selecting synthetic biology tools |
| title_full_unstemmed | SynBioTools: a one-stop facility for searching and selecting synthetic biology tools |
| title_short | SynBioTools: a one-stop facility for searching and selecting synthetic biology tools |
| title_sort | synbiotools a one stop facility for searching and selecting synthetic biology tools |
| topic | Synthetic biology Computational tool Database Tool retrieval Tool registry Table extraction |
| url | https://doi.org/10.1186/s12859-023-05281-5 |
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