Design tools for engineering biology

Our lab leads and participates in a large variety of collaborative projects with research groups worldwide, contributing to a growing portfolio of tools and workflows for synthetic biology and metabolic engineering.

Pathway design

DetSpace

Engineering detectable pathways for bio-based chemical production.

Galaxy-SynBioCAD

Synthetic biology design automation tools in Galaxy workflows.

RetroPath2.0

A retrosynthesis workflow for metabolic engineers,

Retropath

Automated pipeline for embedded metabolic circuits.

SensiPath

Computer-aided design of sensing-enabling metabolic pathways.

XTMS

Pathway design in an eXTended metabolic space.

MetaHype

Metabolic pathway enumeration for heterologous production of chemicals.

Protein design

SelenzymeRF

Enzyme selection for unbalanced biochemical reactions.

Selenzyme

Enzyme selection tool for pathway design.

RetroRules

 A database of reaction rules for engineering biology.

Promis

Enzyme Promiscuity Prediction.

Molecular design

SensBio

 Allosteric transcription factor-based biosensor design.

EcoliTox

Chemical intracellular toxicity prediction in bacteria.

MolSig

Stereo signature molecular descriptor.

Genetic design

SelProm

A queryable and predictive expression vector selection tool for Escherichia coli.

SynBioPython

An open-source software library for synthetic biology.

PartsGenie

An integrated tool for optimizing and sharing synthetic biology parts.