MoSeC - Model to Sequence Converter

Model-based design is common in engineering synthetic biological systems. Models of such systems contain information about used biological entities, relationships between them and description of the system dynamic behaviour. When models are annotated with information about genetic elements needed to build a the system, the conversion between the model and a DNA sequence ready for synthesising, can be automated.

MoSeC converts SBML and CellML models constructed using Standard Virtual Parts to DNA sequence in GenBank, EMBL or SBOL format. The models are initially represented as graphs and the flow of information at the transcriptional and translational levels is used to find the order of parts.

Download

MoSeC is written in Java and requires version 7 or later. To run MoSeC, download the binaries, unzip it, and then run it with:

java -jar MoSeC.jar

More usage examples and a detailed description can be found in the manual.

Publications

• DOI BibTeX
  G. Misirli, J.S. Hallinan, T. Yu, J.R. Lawson, S.M. Wimalaratne, M.T. Cooling, A. Wipat
  Model annotation for synthetic biology: automating model to nucleotide sequence conversion
  in Bioinformatics, 27(7):973-979, April 2011

  @ARTICLE{Misirli2011,
    title = {Model annotation for synthetic biology: automating model to nucleotide sequence conversion},
    author = {Misirli, G. and Hallinan, J. S. and Yu, T. and Lawson, J. R. and Wimalaratne, S. M. and Cooling, M. T. and Wipat, A.},
    year = 2011,
    doi = {10.1093/bioinformatics/btr048},
    month = apr,
    journal = {Bioinformatics},
    volume = {27},
    number = {7},
    pages = {973--979}
  }