Retropath: automated pipeline for embedded metabolic circuits

ACS Synth Biol. 2014 Aug 15;3(8):565-77. doi: 10.1021/sb4001273. Epub 2013 Oct 16.


Metabolic circuits are a promising alternative to other conventional genetic circuits as modular parts implementing functionalities required for synthetic biology applications. To date, metabolic design has been mainly focused on production circuits. Emergent applications such as smart therapeutics, however, require circuits that enable sensing and regulation. Here, we present RetroPath, an automated pipeline for embedded metabolic circuits that explores the circuit design space from a given set of specifications and selects the best circuits to implement based on desired constraints. Synthetic biology circuits embedded in a chassis organism that are capable of controlling the production, processing, sensing, and the release of specific molecules were enumerated in the metabolic space through a standard procedure. In that way, design and implementation of applications such as therapeutic circuits that autonomously diagnose and treat disease, are enabled, and their optimization is streamlined.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Alzheimer Disease / metabolism
  • Biomarkers / metabolism
  • Biosensing Techniques
  • Epilepsy / metabolism
  • Escherichia coli / metabolism
  • Humans
  • Metabolic Networks and Pathways*
  • Software*
  • Synthetic Biology / methods*
  • Transcription Factors / metabolism


  • Biomarkers
  • Transcription Factors