Tools

A growing portfolio of synbio-CAD tools where I have been involved in the development, test and validation in the last 10 years:


  • Galaxy-SynBioCAD: Synthetic Biology Design Automation tools in Galaxy workflows.
  • RetroRules: A database of reaction rules for engineering biology, Nucleic Acids Research.
  • SelProm: A Queryable and Predictive Expression Vector Selection Tool for Escherichia coli, ACS Synth Bio.
  • Selenzyme: Enzyme Selection Tool for Pathway Design.
  • RetroPath2.0: A retrosynthesis workflow for metabolic engineers, Metab. Eng.
  • SensiPath: Computer-aided Design of Sensing-enabling Metabolic Pathways, Nucleic Acids Research.
  • XTMS: Pathway Design in an eXTended Metabolic Space, Nucleic Acids Research (Featured in Cell)
  • Retropath: Automated Pipeline for Embedded Metabolic Circuits, ACS Synth Biol.
  • MolSig: Stereo Signature Molecular Descriptor, J Chem Info Model.
  • MetaHype: Metabolic Pathway Enumeration for Heterologous Production of Chemicals.
  • EcoliTox: Chemical Intracellular Toxicity Prediction in Bacteria.
  • Promis: Enzyme Promiscuity Prediction.