iBioSim/conversion/README.md

The conversion package currently supports four types of data conversion and VPR API model generation.

1. Design to modeling:
   a. SBOL2SBML
   b. CelloModeling
2. Modeling to Design: SBML2SBOL
3. Interconversion supported by the libSBOLj2 library: SBOL1 to SBOL2

SBOL2SBML and SBML2SBOL can be build as a standalone JAR. There is also a main Java Converter.java file that supports all four types of conversion.

How to use it:

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

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

where

Required	Description
inputFile	full path to input file

Options	Description
-b	check best practices.
-cf	The name of the file that will be produced to hold the result of the second SBOL file, if SBOL file diff was selected.
-d	display detailed error trace
-e	The second SBOL file to compare to the main SBOL file.
-esf	Export SBML hierarchical models in a single output file.
-f	continue after first error.
-i	allow SBOL document to be incomplete.
-l	specifies language (SBOL1/SBOL2/GenBank/FASTA/SBML) for output (default=SBOL2). To output FASTA or GenBank, no SBOL default URI prefix is needed.
-mf	The name of the file that will be produced to hold the result of the main SBOL file, if SBOL file diff was selected.
-o	specifies the full path of the output file produced from the converter
-no	indicate no output file to be generated from validation. Instead, print result to console/command line.
-oDir [value]	output directory when SBOL to SBML conversion is performed and multiple SBML files are produced for individual submodels
-p [value]	default URI prefix to set an SBOLDocument
-rsbml [value]	The full path of external SBML files to be referenced in the SBML2SBOL conversion
-rsbol [value]	The full path of external SBOL files to be referenced in the SBML2SBOL conversion
-s [value]	select only this object and those it references
-t [value]	uses types in URIs
-v [value]	mark version of data objects created during conversion
-Cello	This option is for dynamic modeling of Cello parts and parametrization

Example run for SBOL to SBML:

  java -jar target/iBioSim-conversion-3.0.0-SNAPSHOT-jar-with-dependencies.jar "-l", "SBML", "-esf", "-p", "http://www.async.ece.utah.edu/", "-oDir", "src/test/resources/edu/utah/ece/async/ibiosim/conversion/SBML_Files/", "-o", "CRISPR_example_out2", "src/test/resources/edu/utah/ece/async/ibiosim/conversion/SBOL_Files/CRISPR_example.xml"

Example run for SBML to SBOL:

  java -jar target/iBioSim-conversion-3.0.0-SNAPSHOT-jar-with-dependencies.jar "-l", "SBOL2", "-p", "http://www.async.ece.utah.edu/", "-o", "src/test/resources/edu/utah/ece/async/ibiosim/conversion/SBOL_Files/INV0_output", "src/test/resources/edu/utah/ece/async/ibiosim/conversion/SBML_Files/INV0.xml"

Pre-installation Requirement(s)

• libSBOLj
• VPR API jar provided from Newcastle Unveristy folks

Building Converter.java:

1. Open up your command line
   1. Navigate to the libSBOLj project and perform mvn install
   2. Navigate to conversion package in iBioSim
      1. type mvn clean to bring in dependencies to iBioSim conversion package
      2. type mvn package to build the JAR

Replacing VPR API jar in iBioSim:

1. Go to the lib folder of the iBioSim directory and delete the old VPR API jar. There should be 3 VPR API jars that should be deleted. For example:
   1. vpr-rdf-util-2.0.4.jar
   2. vpr-sbol-util-2.0.4.jar
   3. vpr.data-2.0.4.jar
2. Add in the 3 new VPR API jars
3. Modify the dependencies in the conversion's pom.xml file to use the new version of the VPR API jars.

Building VPR API for iBioSim GUI:

1. Open up your command line
2. Navigate to conversion package in iBioSim
   1. type mvn clean to bring in dependencies to iBioSim conversion package
   2. type mvn install to build the JAR
   3. type mvn update to update iBioSim workspace