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 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.

MCF2Chem: A manually curated knowledge base of biosynthetic compound production

“…A list of all microbes was obtained from the National Center for Biotechnology Information (NCBI) [ 35 ]. After manually filtering the titles and abstracts, 268 reviews were obtained (Additional file 1 : Table S1), and data from these reviews were extracted using SCITE [ 36 ] before being manually curated. Based on the reference columns in review tables, direct references to each record were obtained and supplemented programmatically or manually.…”

A new era of synthetic biology—microbial community design

“…To make predictive models, we need a thorough quantitative understanding of the parts and the properties emerging from their interaction to be able to combine them, designing more complex systems. Most recently, great effort has been put into integrating modelling to instruct synthetic biology approaches, in as much the same way as predictive models guide engineers to design new technical devices expanding the range of available tools [ 22 , 23 ].…”

“…Communities have unique catalytic activities and can use complex substrates by compartmentalization of pathways and distribution of molecular burden. We now have the synthetic biology tools and approaches at hand that allow us to construct and control communities by engineering their communication, gene expression, and metabolic interactions [ 23 ]. Controlling the behaviour of individual species within a community has consequences for population dynamics.…”