ArticleBioinformatics (Oxford, England)2011
Model annotation for synthetic biology: automating model to nucleotide sequence conversion.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop.Synthetic biology (Oxford, England) · 2023Article
- The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering.Frontiers in bioengineering and biotechnology · 2020Article
- Harmonizing semantic annotations for computational models in biology.Briefings in bioinformatics · 2019Review
- A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference.ACS synthetic biology · 2018Article
- Design Automation in Synthetic Biology.Cold Spring Harbor perspectives in biology · 2017Review
- Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization.Bioinformatics (Oxford, England) · 2016Article
- Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants.Frontiers in bioengineering and biotechnology · 2015Review
- The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.Nature biotechnology · 2014Article
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Authors and funding
7 authors.
Funding
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Abstract
motivationThe 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.
resultsWe 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. AVAILABILITY: The software is available from the authors' web site http://research.ncl.ac.uk/synthetic_biology/downloads.html.
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