Synthetic Biology

A list of tools, databases and methods for synthetic biology.

Antibiotics and Secondary Metabolite Analysis Shell (antiSMASH)

A tool which allows the user to search through up to a whole genome and find secondary metabolite synthesis genes. It works on plant, bacterial and fungal sequences.

From the abstract: The first comprehensive pipeline capable of identifying biosynthetic loci covering the whole range of known secondary metabolite compound classes (polyketides, non-ribosomal peptides, terpenes, aminoglycosides, aminocoumarins, indolocarbazoles, lantibiotics, bacteriocins, nucleosides, beta-lactams, butyrolactones, siderophores, melanins and others). It aligns the identified regions at the gene cluster level to their nearest relatives from a database containing all other known gene clusters, and integrates or cross-links all previously available secondary-metabolite specific gene analysis methods in one interactive view.


A professionally staffed public-benefit facility which was initiated by a grant from the National Science Foundation (NSF) and is led by bioengineers from UC Berkeley and Stanford University. Tools include software for Multiple RNA Folding and a BIOFAB edition of Clotho for synthetic biology computer aided design. A BIOFAB studio for synthetic biology computer aided design is in the works. 

Cell Modeller

CellModeller is a framework for modelling multicellular systems, including biophysics, regulatory dynamics, intercellular signalling, and rule-based behaviours. It is implemented using OpenCL, a parallel computation standard, allowing very large numbers of cells to be simulated.

Cell Modeller was first published in Dupay et al., 2007. A System for Modelling Cell –Cell Interactions during Plant Morphogenesis. Annals of Botany 1– 11 doi:10.1093/aob/mcm235

Clone qc

This resource is described in detail in a paper

From the abstract: Here we present CloneQC, a lightweight software pipeline available as a free web server and as source code that performs quality control on sequenced clones. Input to the server is a list of desired sequences and forward and reverse reads for each clone. The server generates summary statistics (error rates and success rates target-by-target) and a detailed report of perfect clones. This software will be useful to laboratories conducting in-house DNA synthesis

CRISPR/Cas genome editing

CRISPR/Cas technology is described on this website.

Three papers demonstrating CRISPR-Cas genome editing technology in plants were published back-to-back in Nature Vol. 31 Issue 8 (2013). 

CRISPR/Cas constructs for plant science are available on Addgene

Gibson Assembly

An online manual for Gibson Isothermal Assembly, including an explanation of the chemistry, a clear workflow, and advice on sourcing materials. 

Gibson Assembly was first published in Gibson et al. 2009, Nature Methods DOI:10.1038/NMETH.1318

Golden Gate, Golden Braid, and MoClo

The Golden Gate DNA assembly method offers standardized, quasi-scarless, multi-part DNA assembly, and is an excellent choice for combinatorial library construction. For background and links, see:

The parts for Golden Gate assembly are now available on Addgene

Golden Gate was originally published in Engler C et al., 2008. A One Pot, One Step, Precision Cloning Method with High Throughput Capability. PLoS ONE 3(11): e3647. doi:10.1371/journal.pone.0003647

The Golden Braid method is adapted from Golden Gate. It is published in Sarrion-Perdigones A et al., 2011. GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules. PLoS ONE 6(7): e21622. doi:10.1371/journal.pone.0021622


GoldenBraid DNA Assembly

GoldenBraid is a modular cloning technique. The GB Cloning website includes protocols and a digital tool to help with assembly. Users can request a starter kit containing the parts required for GB cloning.

GoldenBraid 2.0 was published in: Sarrion-Perdigones A, Vazquez-Vilar M, Palací J, Castelijns B, Forment J, Ziarsolo P, Blanca J, Granell A, Orzaez D. (2013) GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology. Plant Physiol. 2013 162: 1618-1631.

Infobiotics workbench is a computational framework implementing a synergy between executable biology, multi-compartmental stochastic simulations, formal model analysis and structural/parameter model optimisation for computational systems and synthetic biology. was first published in 

Blakes et al. 2011. The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology. Bioinformatics doi: 10.1093/bioinformatics/btr571


Liverpool GeneMill

The Liverpool GeneMill has been funded by the BBSRC with an initial investment of £3M to establish a facility for the rapid high throughput construction and testing of synthetic DNA constructs. Liverpool GeneMill removes complexity for the end user, providing end-to-end design, construction and phenotypic validation of libraries of gene constructs for academic and industrial applications.

  • construct design
  • DNA synthesis (sequence verified); from plasmid libraries to artificial chromosomes
  • genome editing tools e.g. CRISPR/Cas9 and TALENs
  • protein design and expression systems (including bacteria, yeast, plant, mammalian and cell-free systems)
  • protein expression and function prototyping
  • scalable fermentation analysis
  • metabolomic / proteomic analyses.


BBSRC funded Synethtic Biology hub. Collaboration between University of Cambridge and the Sainsbury laboratory in Norwich.

Providing open technologies for plant synethtic biology. Many available resources.


From the website: Pcomp is a database of rationally designed Peptide components for synthetic biology. Entries in Pcomp are tectons that form self-assembled units. These have the potential to combine into functional assemblies and further organised or encapsulated into systems.

Plasmids from The Sainsbury Laboratory

This database contains a list of molecular parts (plasmids) in use at SynBio@TSL. The database currently contains 95 backbones and tools and 135 standard parts for plants.

Many plasmids in the database are available from the non-profit organisation, AddGene. Unpublished plasmids not available through AddGene are available but may not have been tested. 


The SynBio@TSL pages are a rich source of information for all things synthetic biology. They include introductions to the field and to specific techniques, guides to synbio tools and resources, and protocols. 

SynBio@TSL YouTube Channel

YouTube channel from SynBio@TSL, featuring a series of videos on parallel gene cloning methods GoldenGate and MoClo.

Synthetic Biology Open Language

From the website: Synthetic Biology Open Language (SBOL) is a software standard for the electronic exchange of specifications and descriptions of genetic parts, devices, modules, systems, and engineered genomes.

Synthetic biology videos

A selection of synthetic biology experts present their research and their idea of synthetic biology at the 2012 New Phytologist workshop on Synthetic Biology. 

TAL effectors

One of the ‘building blocks’ commonly used in synthetic biology. Free to use with full instructions on how to construct and customize your own system. A kit can be bought if you prefer.