SynBioTools: a one-stop facility for searching and selecting synthetic biology tools

• Published in: BMC bioinformatics Vol. 24; no. 1; p. 152
• Main Authors: Cai, Pengli, Liu, Sheng, Zhang, Dachuan, Xing, Huadong, Han, Mengying, Liu, Dongliang, Gong, Linlin, Hu, Qian-Nan
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 17.04.2023; BioMed Central; BMC
• Subjects: Analysis; Artificial intelligence; Bioinformatics; Biological effects; Biology; Citations; Computational biology; Computational Biology - methods; Computational tool; Computer applications; Data processing; Databases, Factual; Experimental methods; Health aspects; High-throughput screening (Biochemical assaying); Metabolism; Metabolites; Methods; Online databases; Proteins; Registries; Research methodology; Retrieval; Searching; Software; Subdivisions; Synthetic Biology; Table extraction; Tables (data); Tool registry; Tool retrieval; Switzerland; Database; Tool registry; Synthetic biology; Computational tool; Tool retrieval; Table extraction
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-023-05281-5

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. 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. 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.