RESOURCESRESOURCES

Synthetic Biology

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

Antibiotics and Secondary Metabolite Analysis Shell (antiSMASH)

http://antismash.secondarymetabolites.org/

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.

BioFAB

http://biofab.org/

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

http://www.plantsci.cam.ac.uk/Haseloff/CellModeller/

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

http://cloneqc.thruhere.net/

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

http://www.addgene.org/CRISPR/plant/

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

http://www.srcf.ucam.org/~wac26/gibson/

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

http://j5.jbei.org/j5manual/pages/23.html

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: http://j5.jbei.org/j5manual/pages/23.html

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

https://gbcloning.org/

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.org

http://www.infobiotics.org/

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. 

Infobiotics.org 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

http://genemill.liv.ac.uk

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.

OpenPlant

http://openplant.org/

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.

Pcomp

http://coiledcoils.chm.bris.ac.uk/pcomp/

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

http://synbio.tsl.ac.uk/?page_id=52

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. 

SynBio@TSL

http://synbio.tsl.ac.uk/

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

https://www.youtube.com/channel/UCUOR6ZqMFxUJlm8VLtmKIEA/feed

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

Synthetic Biology Open Language

http://www.sbolstandard.org/

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

http://www.youtube.com/playlist?list=PLylDstki6x-p3LHwkTKldrdQBgvWzc6W0

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

http://taleffectors.com/

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.