Software for Synthetic Biology Workflows Workshop | AIChE

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This workshop is a tutorial session intended to introduce participants to recent software tools and how they can be used to address common challenges in synthetic biology. The first half of the workshop will introduce a number of recent software tools and key underlying technologies, then show how these can be combined and incorporated into effective organism engineering workflows. In the second half, participants will work hands-on with the tools in groups, with the instructors assisting them in applying tools hands-on to address prototypical example problems and/or challenges from their own work. For the second half, participants are strongly encouraged to bring a laptop with network access.

This workshop will be free for attendees of SEED 2018. There will be a small fee if you wish to attend this workshop without attending SEED.

Preliminary Agenda:

Introduction: workflows and enabling technologies (Jacob Beal, Raytheon BBN Technologies)

Tool Introductions:

  • BEI ICE (Nathan Hillson, JBEI/Berkeley)
  • SynBioHub, iBioSim, and SBOLDesigner (Tramy Nguyen, University of Utah)
  • Cello (Shuyi Zhang, MIT)
  • Operon Calculator and RBS Library Calculator (Howard Salis, Penn State)
  • BOOST (Ernst Oberortner, Joint Genome Institute)
  • TASBE Analytics (Jacob Beal, Raytheon BBN Technologies)

Coffee Break

Hands-on Workflows Session (Kevin Clancy, Synthetic Genomics) 

For questions, contact


  • Dr. Jacob Beal, Raytheon BBN Technologies
  • Dr. Kevin Clancy, Synthetic Genomics, Inc.
  • Dr. Ernst Oberortner, DOE Joint Genome Institute

Check out the SBOL (Synthetic Biology Open Language) website here.