SynBiopython: An open-source software library for Synthetic Biology

Jing Wui Yeoh, Neil Swainston (Corresponding Author), Peter Vegh, Valentin Zulkower, Pablo Carbonell, MacIej B. Holowko, Gopal Peddinti, Chueh Loo Poh (Corresponding Author)

Research output: Contribution to journalArticleScientificpeer-review

Abstract

Advances in hardware automation in synthetic biology laboratories are not yet fully matched by those of their software counterparts. Such automated laboratories, now commonly called biofoundries, require software solutions that would help with many specialized tasks such as batch DNA design, sample and data tracking, and data analysis, among others. Typically, many of the challenges facing biofoundries are shared, yet there is frequent wheel-reinvention where many labs develop similar software solutions in parallel. In this article, we present the first attempt at creating a standardized, open-source Python package. A number of tools will be integrated and developed that we envisage will become the obvious starting point for software development projects within biofoundries globally. Specifically, we describe the current state of available software, present usage scenarios and case studies for common problems, and finally describe plans for future development. SynBiopython is publicly available at the following address: http://synbiopython.org.

Original languageEnglish
Article numberysab001
JournalSynthetic Biology
Volume6
Issue number1
DOIs
Publication statusPublished - 2021
MoE publication typeA1 Journal article-refereed

Keywords

  • Automation
  • Biofoundries
  • Open-source
  • Software
  • Synthetic Biology

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