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

• Published in: Journal of biological engineering Vol. 6; no. 1; p. 14
• Main Authors: Hesselman, Matthijn C, Koehorst, Jasper J, Slijkhuis, Thijs, Odoni, Dorett I, Hugenholtz, Floor, van Passel, Mark W J
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 04.09.2012; BioMed Central; BMC
• Subjects: Algorithms; Binding sites; BioBrick parts; Bioengineering; Biology; Circuits; Cloning; Computer engineering; Design; Genetic circuit; Genetic transcription; Laboratorium voor Microbiologie; Letters to the Editor; Microbiological Laboratory; Microbiologie; Microbiology; Molecular biology; Synthetic Biology; Systeem en Synthetische Biologie; Systems and Synthetic Biology; Transcription units; VLAG; Web site management software; WIMEK
• ISSN: 1754-1611; 1754-1611
• DOI: 10.1186/1754-1611-6-14

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) 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.