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SynBio2Easy-a biologist-friendly tool for batch operations on SBOL designs with Excel inputs.
Tomasz Zieliński1, Johnny Hay2, Andrew Romanowski1
1SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
Synthetic Biology (Oxford, England)
|March 30, 2022
Summary
SynBio2Easy streamlines synthetic biology data sharing by automating operations on multiple designs using Excel. This tool facilitates the generation and deposition of large construct libraries, making FAIR data principles more accessible for researchers.
Area of Science:
- Synthetic Biology
- Bioinformatics
- Data Management
Background:
- Implementing Findable, Accessible, Reusable, and Interoperable (FAIR) principles in research data management requires significant expertise, resources, and tools.
- The Synthetic Biology Open Language (SBOL) standard facilitates FAIR data sharing for synthetic biology constructs, often utilized via platforms like SynBioHub.
- Manual curation of large synthetic biology design libraries is time-consuming and presents a barrier to data sharing for researchers.
Purpose of the Study:
- To present SynBio2Easy, a tool designed to simplify and automate the management of multiple SBOL designs.
- To enable easier interaction with repositories like SynBioHub for synthetic biology data sharing.
- To reduce the manual effort required for curating and depositing large datasets of synthetic biology constructs.
Main Methods:
- Developed SynBio2Easy, a software tool that uses Microsoft Excel tables for metadata input to automate operations on SBOL designs.
- Implemented utilities for SBOL document manipulation, including library generation and bulk deposition to SynBioHub.
- Utilized the tool to generate and deposit a collection of 3661 cyanobacterium *Synechocystis* plasmids into SynBioHub.
Main Results:
- Successfully generated and deposited 3661 *Synechocystis* plasmid designs into the SynBioHub repository using SynBio2Easy.
- Demonstrated the tool's capability to streamline the creation of plasmid libraries from a template.
- Automated the annotation of SBOL component definitions with authorship and notes during the process.
Conclusions:
- SynBio2Easy significantly reduces the burden of manual data curation and deposition for synthetic biology researchers.
- The tool promotes the adoption of FAIR data principles by simplifying complex data management tasks.
- Evaluations during development led to proposals for improving the SBOL ecosystem and SynBioHub platform for enhanced user experience.
