Autonomous Objects and Bottom-Up Composition in ZOO Applied to a Case Study of Biological Reactivity

1. Amálio, N., Polack, F., Stepney, S.: An object-oriented structuring for Z based on views. In: Treharne, H., King, S., C. Henson, M., Schneider, S. (eds.) ZB 2005. LNCS, vol. 3455, pp. 262–278. Springer, Heidelberg (2005)

   Google Scholar 

2. Amálio, N.: Generative frameworks for rigorous model-driven development. Ph.D. thesis, Dept. Comp. Science, Univ. of York (2007)

   Google Scholar 

3. Kam, N., Harel, D., Cohen, I.R.: Modeling biological reactivity: Statecharts vs. boolean logic. In: Proc. Int. Conf. on Systems Biology (ICSB 2001) (2001)

   Google Scholar 

4. Booch, G., Rumbaugh, J., Jacobson, I.: The Unified Modeling Language User Guide. Addison-Wesley, Reading (1999)

   Book  Google Scholar 

5. Gamma, E., Helm, R., Johnson, R., Vlissides, J.: Design Patterns: Elements of Resusable Object-Oriented Software. Professional Computing. Addison-Wesley, Reading (1995)

   Google Scholar 

6. Larman, C.: Applying UML and patterns: an introduction to object-oriented analysis and design (1998)

   Google Scholar 

7. Kam, N., Harel, D., Cohen, I.R.: The immune system as a reactive system: Modeling T cell activation with statecharts. In: VLFM 2001 (2001)

   Google Scholar 

8. Kaufman, M., Andris, F., Leo, O.: A logical analysis of T cell activation and anergy. Proc. Natl. Acad. Sci. USA 96(7) (1999)

   Google Scholar 

9. Harel, D.: Statecharts: A visual formalism for complex systems. Science of Computer Programming 8, 231–274 (1987)

   Article  MATH  MathSciNet  Google Scholar 

10. Woodcock, J., Davies, J.: Using Z: Specification, Refinement, and Proof (1996)

    Google Scholar 

11. Amálio, N., Polack, F., Zhang, J.: Zoo specification of T-cell statecharts (2008), http://www-users.cs.york.ac.uk/~fiona/PUBS/zoo-tcell-statecharts.pdf

12. Amálio, N., Stepney, S., Polack, F.: Formal Proof from UML Models. In: Davies, J., Schulte, W., Barnett, M. (eds.) ICFEM 2004. LNCS, vol. 3308, pp. 418–433. Springer, Heidelberg (2004)

    Google Scholar 

13. Saaltink, M.: The Z/EVES system. In: Bowen, J., Hinchey, M. (eds.) ZUM 1997. LNCS, vol. 1212, pp. 72–85. Springer, Heidelberg (1997)

    Chapter  Google Scholar 

14. Zhang, J.: Extending an approach to formalize diagrammatic model: Analysis of Harel’s T cell model. Master’s thesis, Dept. Comp. Science, Univ. of York (2006)

    Google Scholar 

15. Amálio, N., Stepney, S., Polack, F.: Modular UML semantics: Interpretations in Z based on templates and generics. In: Van, H.D., Liu, Z. (eds.) FACS 2003 Int. Workshop, vol. 284, pp. 81–100. UNU/IIST Technical Report (2003)

    Google Scholar 

16. Borgida, A., Mylopoulos, J., Reiter, R.: On the frame problem in procedure specifications. IEEE Trans. on Softw. Eng. 21(10), 785–798 (1995)

    Article  Google Scholar 

17. Amálio, N., Stepney, S., Polack, F.: A formal template language enabling meta-proof. In: Misra, J., Nipkow, T., Sekerinski, E. (eds.) FM 2006. LNCS, vol. 4085, pp. 252–267. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

18. Stepney, S., Polack, F.A.C., Turner, H.R.: Engineering emergence. In: ICECCS 2006, pp. 89–97. IEEE Computer Society, Los Alamitos (2006)

    Google Scholar 

19. Liu, J., Tsui, K.: Toward nature-inspired computing. Commun. ACM 49(10), 59–64 (2006)

    Article  Google Scholar 

Download references