SBOLDesigner

SBOLDesigner is a simple, biologist-friendly CAD software tool for creating and manipulating the sequences of genetic constructs using the Synthetic Biology Open Language (SBOL) 2.2 data model.  Throughout the design process, SBOL Visual symbols, a system of schematic glyphs, provide standardized visualizations of individual parts.  SBOLDesigner completes a workflow for users of genetic design automation tools.  It combines a simple user interface with the power of the SBOL standard and serves as a launchpad for more detailed designs involving simulations and experiments.  Some features in SBOLDesigner are SynBioHub integration, local repositories, importing of parts/sequences from existing files, import and export of GenBank and FASTA files, extended role ontology support, the ability to partially open designs with multiple root ComponentDefinitions, backward compatibility with SBOL 1.1, and versioning.  SBOLDesigner is made freely available under the Apache 2.0 license.

Features

  • Read/Write of SBOL 2.0
  • Hierarchy
  • Orientation
  • Generic/user defined parts
  • Multiple designs in a single SBOL file
  • Importing Parts/Sequences from other SBOL files
  • Registries (SynBioHub, built-in parts, working document, local repositories)
  • Web of Registries integration
  • Provenance
  • Versioning
  • Import/Export (GenBank, FASTA, SBOL 1.1, SBOL 2.0)
  • Export of SBOL Visual 2 glyphs and overlays
  • Combinatorial Design

Installation Files

To run the latest release, download and double-click on the pre-built jar found here.  Make sure you have an updated installation of Java.
Please post feedback/bugs/feature requests to my issue tracker.
Additionally, the GitHub repository can be found here.

Other Useful Information

These videos show a synthetic biology workflow using SBOLDesigner embedded in iBioSim.  (Part 1, Part 2)

This paper goes over SBOLDesigner’s backend and use of SBOL 2.

Credits

This tool is currently being developed by Michael Zhang in the Myers research group at the University of Utah.  SBOLDesigner started at the University of Washington in collaboration with Clark & Parsia by Michal Galdzicki, Bryan Bartley, Sean Sleight, Evren Sirin, and John Gennari.