A parser for systems biology models published in a table form that produces standardized files, such as SBML.
This project provides useful Java™ classes to read systems biology models from character-separated table files and writes them to standardized community formats, such as SBML using the JSBML library.
One example use case to try out this package would be the the model iCW773 that was given in the form of two tables in the publication. Initially, the code in this package has been tailored to the format of this specific model, but could be useful in other circumstances, too.
To build an executable from this project run the following:
mvn assembly:assembly package
It will automatically create the file table2model-1.0-jar-with-dependencies.jar within the target/ directory of this project.
Run the executable as follows:
java -jar target/table2model-1.0-jar-with-dependencies.jar /path/to/metabolites.csv /path/to/reactions.csv /path/to/output.xml