Xholon - SBML and Biochemical Networks

Xholon - SBML and Biochemical Networks

Xholon is an open source general-purpose modeling and simulation tool that supports importing of Systems Biology Markup Language (SBML) 2.1, and limited exporting. It can, for example, read files exported by COPASI. Xholon can also read biological and other models created using Unified Modeling Language (UML 2) tools. Xholon is written in Java, and uses libSBML. The previously separate Cellontro project, with a focus on biology modeling, has now been made part of Xholon. The intent is to gradually integrate the different types of models and simulations that Xholon supports, for example UML and SBML.

To try using Xholon with your own models or on a few sample models that are included with Xholon:

  • Download Xholon.
  • Install Xholon by unzipping or untarring the downloaded file.
  • Look through README.txt in the Xholon directory. This will tell you how to start Xholon and run applications.
  • Run some of the sample applications that have been transformed from SBML, and that were originally modeled using Copasi. Start the Xholon GUI, and select File --> Open. Open one of the models in the sbml directory. Other biochemical network models that were created natively in Xholon are in the cellontro directory. Each model includes a web page with information about it. Once a model is opened, select Help --> Information from the Xholon GUI.
  • There are also several biochemical models in the xmiapps directory. All of these have been modeled using a UML tool and were then transformed to Xholon format. See the models that start with Rcs_ .
  • Transform your own models from SBML to Xholon format, and then execute them using the Xholon runtime framework. To transform a model, select File --> Import --> Sbml , and then select one of the models listed. You should then see a status message in the console window of the Xholon GUI. You will then need to compile the generated Java code, and can then run the model using the Xholon GUI.

You might also want to look at the related Cellontro website, and at a list of related publications.