Xholon - Membrane Computing
Xholon - Membrane Computing
Xholon is an open source general-purpose modeling, transformation and simulation tool, based on XML and Java, that supports the Unified Modeling Language (UML 2.1), systems biology modeling including SBML, other types of modeling, and many of the features needed to support P Systems (Membrane Computing). Like P Systems, Xholon is based on a concept of hierarchically organized structures, a concept it borrows from biology, and from the Unified Modeling Language (UML 2) where it is known as composite structure. Xholon focuses especially on integration of various approaches. It can, for example, model the same application either as a finite state machine or as a P System. The Xholon download includes numerous example applications, including six that re-implement models found in the membrane computing literature, and one from the related field of brane calculi.
To try out Xholon by running the membrane computing sample models or by developing your own models:
- 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 P System models. Start the Xholon GUI, and select File --> Open --> memcomp. Open one of the models shown below, by first going into the directory of that name, and selecting the _xhn.xml file of that name (for example, File --> Open --> memcomp --> CoopPSys00ex0 --> CoopPSys00ex0_xhn.xml). Each model includes a web page with information about it. Once a model is opened, select Help --> Information from the Xholon GUI.
- CoopPSys00ex0 - Paun, Gh. (2000). Computing with Membranes. Journal of Computer and System Sciences, 61, 1. (Example on p. 117+)
- CoopSys02ex32_1 - Paun, Gh. (2002). Membrane Computing. An Introduction, Springer-Verlag. (First example in section 3.2.)
- CoopSys02ex343_1 - Paun, Gh. (2002). Membrane Computing. An Introduction, Springer-Verlag. (First example in section 3.4.3)
- CoopSys02ex343_2 - Paun, Gh. (2002). Membrane Computing. An Introduction, Springer-Verlag. (Second example in section 3.4.3)
- SymAnti02ex41 - Paun, Gh. (2002). Membrane Computing. An Introduction, Springer-Verlag. (Example in section 4.1)
- Fsm06ex1 - a model of a simple finite state machine (FSM) implemented as a P System, and separately as a FSM.
- BraneCalc1 - a Xholon implementation of a Brane Calculus (membrane calculus) model presented in: Cardelli, L. and Paun, Gh. (2005). A universality result for a (mem)brane calculus based on mate/drip operations.
To create a model of your own, look through these sample models, and also look at the various tutorials and other information available in the download and at the Xholon web site.