MoSeC

Project Description

MoSeC is a Java application for synthetic biology design that takes a model annotated with the DNA sequence information of genetic elements and converts it into a DNA sequence. Both CellML and SBML models constructed using SVPs can be converted into standard GenBank, EMBL or SBOL files ready for synthesising.

Model-based design in common place in Engineering and models also form an excellent blueprint for synthetic biological systems. Modelling languages such as CellML and SBML provide information about the biological entities in a design, the relationships between them and mathematical models that can be simulated to study the dynamic behaviour of the system . Models can also be annotated with information including the genetic elements necessary to build a system, biological context in a computationally accessible fashion.

MoSeC

In order to facilitate the automation of the conversion of dynamic models into DNA sequences, SVPs are annotated with machine-readable metadata. Using this information, modelling entities that are mapped to sequence features can be distinguished from other entities in dynamic models. In addition, metadata includes information about DNA sequences of parts represented by SVPs. These annotations are stored in RDF/XML format in the XML structure of CellML and SBML models. In order to derive the ordering of biological parts from dynamic models, graph-based analysis techniques are used. The models are initially represented as graphs and the flow of information at the transcriptional and translational levels is used to derive the ordering of parts.

Download

MoSeC1.2 ( Requires Java 7) :
Click here to download MoSeC 1.2.
Click here to download the supplementary documents.

To run the application, unzip MoSeC1.2.zip, change into the MoSeC directory and type the following on the command line:

java –jar “MoSeC.jar”

MoSeC can also be launched by double clicking on the MoSeC.jar file.

For more details please refer to the supplementary file.

MoSeC1.1:
Click here to download MoSeC 1.1.
Click here to download the supplementary documents.

MoSeC1.0:
Click here to download MoSeC 1.0.
MoSeC1.0 requires libSBML to convert SBML files into DNA sequences.