iBioSim/synthesis

The synthesis package currently performs technology mapping on combinational designs.

How to use it:

After building the executable jar, you need to invoke the following command:

  java -jar target/iBioSim-synthesis-3.0.0-SNAPSHOT-jar-with-dependencies.jar [options] input

where

Required	Description
-lf	full path to the library file containing set of genetic gates needed for technology mapping.
-sf	full path to the specification file to performing technology mapping.
-sbml	perform SBML Technology Mapping
-sbol	perform SBOL Technology Mapping
-o	name of output file along with full path of where output file will be written to.
-osbml	produce solution for technology mapping in SBML format.
-osbol	produce solution for technology mapping in SBOL format.

Options	Description
-p [value]	SBOL URI prefix needed to set the SBOLDocument when converting the technology mapping solution to the desired SBOL or SBML data format.
-ld [value]	directory to multiple SBOL or SBML library files
-dot [value]	produced SBOL technology mapping solution in dot format.

Example run for SBML Technology Mapping:

  java -jar target/iBioSim-conversion-3.0.0-SNAPSHOT-jar-with-dependencies.jar "-lf", "", "-sf", "", "-sbml", "-osbml", "-o", "src/test/resources/edu/utah/ece/async/ibiosim/synthesis/SBML_Files/sbml_techmap_sol"

Example run for SBOL Technology Mapping:

  java -jar target/iBioSim-conversion-3.0.0-SNAPSHOT-jar-with-dependencies.jar