iBioSim/learn

iBioSim Learn

The learn project includes parameter estimation and a regulatory network learning method from time-series data based on the GeneNet procedure.

How to use it:

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

  java -jar target/iBioSim-learn-3.0.0-SNAPSHOT-jar-with-dependencies.jar [-e] [-l ...] input directory

where

• input is an arbitrary SBML file
• directory is the location of the time-series data
• -e is a flag to perform parameter estimation. Default is GeneNet.
• -l ... is a flag to specify which parameters need to be estimated, where the value is a comma separated list of parameter ids (e.g., "p1,p2,p3").