5.4 Formulation and utilization of a real time UML description of hybrid electronic chemical cell processing

The basic objects and classes will be developed by BioMIP including the UML-diagrams. The fuzzy and incomplete physico-chemical information shall be encapsulated and built into a class-hierarchy of UML-RT (unified modeling language, real time[1]) diagrams. These diagrams then serve as an interface to full programmability of ECCells via abstract objects in a concurrent programming language. Utilizing CellAK[2] or similar tools will embed the ECCell information processing language in a systematic work describing compartmentalized information processing in systems biology.  SBML[3] (systems-biology-markup-language) and its spatial extensions, and on developments in membrane molecular computing paradigms[4] are easily connected. Specific features of the ECCell information processing language will include feedback control loops, local phase transitions, molecular self-assembly and integrated image processing.

[1]       Selic, B., Gullekson, G., Ward, P., 1994. Real-time Object-Oriented Modeling. John Wiley & Sons, New York.

[2]       Webb, K. , White, T., 2005, UML as a cell and biochemistry modeling language, BioSystems 80:283-3302

[3]       http://sbml.org

[4]       Paun, Gh., 2004, Introduction to Membrane Computing, First Brainstorming Workshop on Uncertainty in Membrane Computing, Palma de Mallorca, Spain, November 2004, 17-65