View source for Headless BioUML

Headless BioUML (or Shell BioUML) is a version of standalone BioUML application without graphic user interface. It allows manipulation with data from repository, import files, work with models, performing numerical simulation and analysis.
All of it can be done through java-script API. It also allows manipulating Java objects via org.mozilla.Rhino library.
Headless BioUML may be used in two ways:

1. As a shell executing input commands. 
Simply run 

 sh ./shell.sh
 
(or shell.bat in Windows) from the directory in which BioUML is installed.

2. To execute script from file run 

 sh ./shell.sh -js.f <PATH_TO_FILE> 

from the directory in which BioUML is installed. Replace <PATH_TO_FILE> with path to file containing script you want to execute.

==Examples==
1. Single simulation.<br>
Here is a simple script example to simulate SBML model and save results into the file

 var model_path = ""; //Here is a path to existing SBML model
 var result_path = ""; //Here is a path to output file
 var diagram = sbml.load("model_path");
 var span = simulationEngine.createSpan(0,100,1); //Create time span from 0 to 100 with step 1
 var result = simulationEngine.simulate(diagram, span); 
 simulationEngine.writeResult(result, result_path, ",", true);

Note:
<b>sbml</b> and <b>simulationEngine</b> are host objects providing API for work with sbml and numerical simulations correspondingly.

To get full list of available methods simply type name of host object.

2. Repeated simulations.<br> 
In previous example, loaded diagram is compiled into java object Model during <b>simulate</b> step. If you run repeated simulations of the same model you may want to perform this step only once as it may be time consuming. In order to do that you need to call simulationEngine.compileModel and then use simulationEngine.simulateModel

 var model_path = ""; //Here is a path to existing SBML model
 var result_path = ""; //Here is a path to output file
 var diagram = sbml.load("model_path");
 var model = simulationEngine.compileModel(diagram) //Compile model object
 var span = simulationEngine.createSpan(0,100,1); //Create time span from 0 to 100 with step 1
 for (var i=0; i<10; i++)
 {
   var result = simulationEngine.simulate(model, span); 
   simulationEngine.writeResult(result, result_path, ",", true); //write results into file result_path. Numeric values are separated with "," symbol
 }