Development of a database and a set of software tools for GoldenBraid

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Marta Vazquez-Vilar, Sarrion-Perdigones A, Forment J, Orzaez D

Instituto de Biologa Molecular y Celular de Plantas. CSIC-UPV, Spain

We are going through a stage where Synthetic Biology is gaining relevance and, although there are many available tools for working in the Synthetic Biology field aimed at bacteria, Plant Synthetic Biology is still emerging. To overcome the existing limitations on the design and construction of new genetic combinations, the GoldenBraid assembly system was improved into a new version, GB2.0, which has strengthen its grammar and has created a collection of standard DNA parts and genetic modules. The GB assembly process, though simple, implies multiple steps to build a multigenic module. The first of them is the adaptation of a sequence to the standard; then, different standard parts can be assembled together in a multipartite reaction. Finally, transcriptional units, as well as preformed modules, can be assembled together in a binary reaction. To manage the growing GBcollection it was necessary to create a database that houses all the data in an organized way. Therefore we created the GBdatabase using PostgreSQL, a powerful database management system. GoldenBraid2.0 offers also the Gbtool-kit, a set of three computational tools that guide the user through the GBassembly process. The first of them, named GBDomesticator, adapts the input DNA sequence provided by the user to the GBstandard. The second tool, named GBMultiAssembler, performs the in silico multipartite assembly of GBparts to create a transcriptional unit (TU). Finally, the last tool is named GBinAssembler, and allows the binary assembly of preformed TUs or modules over the GoldenBraid loop to produce multigenic structures. The GBdatabase and the GBtool-kit are presented in a website using Django, a Python web framework that supports rapid design and development of web based applications. The development of this project shows that synthetic biology is an interdisciplinary field that needs from the computational science to exploit all its potential.