Model annotation for synthetic biology: Automating model to nucleotide sequence conversion

Goksel Misirli, Jennifer S. Hallinan, Tommy Yu, James R. Lawson, Sarala M. Wimalaratne, Michael T. Cooling, Anil Wipat*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

24 Citations (Scopus)
9 Downloads (Pure)

Abstract

Motivation: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the assembly of models of individual parts such as promoters, ribosome binding sites and coding sequences. These low level models are combined to produce a dynamic model of a larger device that exhibits a desired behaviour. The larger model then acts as a blueprint for physical implementation at the DNA level. However, the conversion of models of complex genetic circuits into DNA sequences is a non-trivial undertaking due to the complexity of mapping the model parts to their physical manifestation. Automating this process is further hampered by the lack of computationally tractable information in most models. Results: We describe a method for automatically generating DNA sequences from dynamic models implemented in CellML and Systems Biology Markup Language (SBML). We also identify the metadata needed to annotate models to facilitate automated conversion, and propose and demonstrate a method for the markup of these models using RDF. Our algorithm has been implemented in a software tool called MoSeC.

Original languageEnglish
Article numberbtr048
Pages (from-to)973-979
Number of pages7
JournalBioinformatics
Volume27
Issue number7
DOIs
Publication statusPublished - Apr 2011
Externally publishedYes

Bibliographical note

Copyright the Author(s) 2011. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Fingerprint

Dive into the research topics of 'Model annotation for synthetic biology: Automating model to nucleotide sequence conversion'. Together they form a unique fingerprint.

Cite this