SynBio2Easy – a biologist-friendly tool for batch operations on SBOL designs with Excel inputs

Tomasz Zielinski, Johnny Hay, Andres Romanowski, Anja Nenninger, Alistair J McCormick, Andrew J Millar

Research output: Contribution to journalArticlepeer-review

Abstract

Practical delivery of Findable, Accessible, Reusable and Interoperable principles for research data management requires expertise, time resource, (meta)data standards and formats, software tools and public repositories. The Synthetic Biology Open Language (SBOL2) metadata standard enables FAIR sharing of the designs of synthetic biology constructs, notably in the repository of the SynBioHub platform. Large libraries of such constructs are increasingly easy to produce in practice, for example, in DNA foundries. However, manual curation of the equivalent libraries of designs remains cumbersome for a typical lab researcher, creating a barrier to data sharing. Here, we present a simple tool SynBio2Easy, which streamlines and automates operations on multiple Synthetic Biology Open Language (SBOL) designs using Microsoft Excel® tables as metadata inputs. The tool provides several utilities for manipulation of SBOL documents and interaction with SynBioHub: for example, generation of a library of plasmids based on an original design template, bulk deposition into SynBioHub, or annotation of existing SBOL component definitions with notes and authorship information. The tool was used to generate and deposit a collection of 3661 cyanobacterium Synechocystis plasmids into the public SynBioHub repository. In the process of developing the software and uploading these data, we evaluated some aspects of the SynBioHub platform and SBOL ecosystem, and we discuss proposals for improvement that could benefit the user community. With software such as SynBio2Easy, we aim to deliver a user-driven tooling to make FAIR a reality at all stages of the project lifecycle in synthetic biology research. Graphical Abstract.

Original languageEnglish
Article numberysac002
Number of pages9
JournalSynthetic Biology
Volume7
Issue number1
DOIs
Publication statusPublished - 26 Jan 2022

Keywords

  • synthetic biology
  • SBOL
  • SynBioHub
  • research data management
  • software tools
  • spreadsheet

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