General Tools

 Molecular Cloning Designer Simulator (MCDS)

  • All-in-one Molecular Cloning and Genetic Engineering Design, Simulation & Management Software for Complex Synthetic Biology and Metabolic Engineering Projects. A fantastic resource for complex synthetic biology and metabolic engineering projects; does all your in-silico design, handles project workflows including experimental notes and flow-on updating, and acts as a project database. And it’s free! Read the paper here and download the software here.

Example project flowchart:

  • For enlargement see slider above, or click on flowchart below.



Xylanase Reporter Gene

  • sXynA: A synthetic xylanase reporter gene for functional analysis. We tested it in plants but it also works fine in E. coli and probably other organisms – the gene is a fungal gene. Can be used in conjunction with the GUSPlus reporter gene for promoter analysis here and get the plasmids here.



  • Green fluorescent protein RNAi construct – can be used to knock down GFP conditionally. Currently under the control of a sucrose-responsive promoter in a yeast expression vector (see here for details), but can be sub-cloned into other constructs for your bespoke applications. Get the plasmid here.


Rapid, High-Throughput Cloning Method

  • A rapid cloning technique for functional analysis of genes and promoters. A bit old-tech but it works. Download it here


High-Throughput Screening for Monoterpene Production

  • A 2,2-diphenyl-1-pycrylhydrazyl (DPPH) based method for high-throughput screening and selection of monoterpene production strains. Read about it here