iBioSim/analysis

iBioSim Analysis

The analysis project encapsulates the different java-based simulation and verification methods that is used in the iBioSim tool.

How to use it:

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

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

where

Required	Description
input	arbitrary SBML, SED-ML, or Combine Archive file

Options	Description
-d [value]	project directory
-p [value]	loads a properties file
-outDir [value]	where the output should be stored
-ti [value]	non-negative double initial simulation time
-tl [value]	non-negative double simulation time limit
-ot [value]	non-negative double output time
-pi [value]	positive double for print interval
-m0 [value]	positive double for minimum step time
-m1 [value]	positive double for maximum step time
-aErr [value]	positive double for absolute error
-sErr [value]	positive double for relative error
-sd [value]	long for random seed
-r [value]	positive integer for number of runs
-sim [value]	simulation type. Options are: ode, hode, ssa, hssa, dfba, jode, jssa.