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Open Access Highly Accessed Letters to the Editor

The Constructor: a web application optimizing cloning strategies based on modules from the registry of standard biological parts

Matthijn C Hesselman1, Jasper J Koehorst1, Thijs Slijkhuis1, Dorett I Odoni1, Floor Hugenholtz12 and Mark W J van Passel13*

Author Affiliations

1 iGEM Wageningen UR, Wageningen University, Wageningen, The Netherlands

2 Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands

3 Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands

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Journal of Biological Engineering 2012, 6:14  doi:10.1186/1754-1611-6-14

Published: 4 September 2012

Abstract

Synthetic biology is an emerging field that combines molecular biology with engineering principles, which requires abstraction levels applied to a modular biological componentry. The Registry of Standard Biological Parts harbours such a repository of standardized parts, and thereby facilitates the combination of complex molecular modules to novel genetic circuits and devices. However, since finding the best parts for a pre-determined genetic design can be time consuming, we devised the Constructor, a web tool that recommends the smallest number of cloning steps for pre-designed circuits, and implements user-defined quality checks.

We present the Constructor ( http://www.systemsbiology.nl/the_constructor webcite) as a constructive web tool that simplifies the in silico assembly of pre-designed gene circuitries from standard parts, reducing both planning and subsequent cloning time.

Keywords:
Synthetic Biology; BioBrick parts; Transcription units; Genetic circuit