STEM: An open source tool for disease modeling

Judith Douglas, Simone Bianco, Stefan Edlund, Tekla Engelhardt, Matthias Filter, Taras Günther, Kun (Maggie) Hu, Emily J Nixon, Nereyda Sevilla, Ahmad Swaid, James Kaufman

Research output: Contribution to journalArticle (Academic Journal)peer-review

15 Citations (Scopus)
274 Downloads (Pure)


Biological engineers often find it useful to communicate using diagrams. These diagrams can include information both about the structure of the nucleic acid sequences they are engineering and about the functional relationships between features of these sequences and/or other molecular species. A number of conventions and practices have begun to emerge within synthetic biology for creating such diagrams, and the Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard to organize, systematize, and extend such conventions in order to produce a coherent visual language. Here, we describe SBOL Visual version 2, which expands previous diagram standards to include new functional interactions, categories of molecular species, support for families of glyph variants, and the ability to indicate modular structure and mappings between elements of a system. SBOL Visual 2 also clarifies a number of requirements and best practices, significantly expands the collection of glyphs available to describe genetic features, and can be readily applied using a wide variety of software tools, both general and bespoke.
Original languageEnglish
Pages (from-to)291-306
Number of pages16
JournalHealth Security
Issue number4
Publication statusPublished - 19 Aug 2019


  • Epidemic management/response
  • Infectious diseases
  • Viral hemorrhagic fevers
  • Influenza
  • Open source epidemiological modeling


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