Verification and Testing Group, DCS, University of Sheffield

1. MIPNETS Liverpool06/2003 Language based approach in biological modelling Marian Gheorghe University of Sheffield Verification and Testing Group, DCS, University of Sheffield

2. Mipnets Liverpool 06/03 Summary Formal languages and biology L systems DNA sequences Membrane computing; X machines Molecular X machines Verification and Testing Group, DCS, University of Sheffield

3. Mipnets Liverpool 06/03 Formal languages/linguistics and biological models FL/Linguistics and biology modern era started in 1950s Both benefited from a mathematical approach Around 30 years of almost independent development 1980s – Chomsky-like approach to molecular biology Later – DNA computing, aqueous computing, membrane computing … Verification and Testing Group, DCS, University of Sheffield

4. Mipnets Liverpool 06/03 L systems L systems introduced as a model of development of simple multicellular organisms, such as blue-green bacteria Anabaena catenula. axiom or initial set of elements set of rewriting rules yields a language A Lindenmayer Verification and Testing Group, DCS, University of Sheffield

5. Mipnets Liverpool 06/03 Simulated model Verification and Testing Group, DCS, University of Sheffield

6. Mipnets Liverpool 06/03 Definition. Example LS = (Vocabulary, Axioms, Rules) Rewriting rules are applied in parallel to all occurrences Axiom: a Rules: a →aba a; aba; abababa; abababababababa … Verification and Testing Group, DCS, University of Sheffield

7. Mipnets Liverpool 06/03 Graphics Axiom: A Rules: A → F[+A][-A]FA F → FF Verification and Testing Group, DCS, University of Sheffield

8. Mipnets Liverpool 06/03 http://www.cpsc.ucalgary.ca/Research/bmv/lstudio/whatis.html Verification and Testing Group, DCS, University of Sheffield

9. Mipnets Liverpool 06/03 The language of genes Verification and Testing Group, DCS, University of Sheffield

10. Mipnets Liverpool 06/03 Language based DNA modelling Verification and Testing Group, DCS, University of Sheffield

11. Mipnets Liverpool 06/03 Definition a gtgc t cacg Verification and Testing Group, DCS, University of Sheffield

12. Mipnets Liverpool 06/03 The language definition Verification and Testing Group, DCS, University of Sheffield

13. Mipnets Liverpool 06/03 The intramolecular language of genes Verification and Testing Group, DCS, University of Sheffield

14. Mipnets Liverpool 06/03 Verification and Testing Group, DCS, University of Sheffield

15. Mipnets Liverpool 06/03 …folded branches a g t c a a t t g t t a a c a g t c Verification and Testing Group, DCS, University of Sheffield

16. Mipnets Liverpool 06/03 Derivation-like S a g t c S S a a t t S g S S S S S S t S t a a S c a g t c S S Verification and Testing Group, DCS, University of Sheffield

17. Mipnets Liverpool 06/03 The formal grammar Verification and Testing Group, DCS, University of Sheffield

18. Mipnets Liverpool 06/03 The grammars of intermolecular structure Verification and Testing Group, DCS, University of Sheffield

19. Mipnets Liverpool 06/03 Language based models of cell Verification and Testing Group, DCS, University of Sheffield

20. Mipnets Liverpool 06/03 Membrane characteristics Verification and Testing Group, DCS, University of Sheffield

21. Mipnets Liverpool 06/03 Cell model (membrane computing) Verification and Testing Group, DCS, University of Sheffield

22. Mipnets Liverpool 06/03 A computation in a membrane system Verification and Testing Group, DCS, University of Sheffield

23. Mipnets Liverpool 06/03 The rules Verification and Testing Group, DCS, University of Sheffield

24. Mipnets Liverpool 06/03 Outcomes Verification and Testing Group, DCS, University of Sheffield

25. k-1 1 …k k m Memory m’ k 1…k… n h-1 (m”,k-1)= (k-1 ,m) ; k (m,k)= (k ,m’) ; m0– initial memory Mipnets Liverpool 06/03 X (Eilenberg) machines State machine with input, memory and output sets - and basic processing functions Verification and Testing Group, DCS, University of Sheffield

26. Mipnets Liverpool 06/03 Molecular X machines Computationally complete Finite state based with input/output streams Structured hierarchically organized memory Provide in every state specific sets of rules acting in parallel in various parts of the memory Verification and Testing Group, DCS, University of Sheffield

27. Mipnets Liverpool 06/03 Variant 1: structured memory distributed rules (Ri,1,…, Ri,m) (Rj,1,…, Rj,m) Verification and Testing Group, DCS, University of Sheffield

28. Mipnets Liverpool 06/03 Variant 2: set of machines derived components Verification and Testing Group, DCS, University of Sheffield

29. Mipnets Liverpool 06/03 Application Verification and Testing Group, DCS, University of Sheffield

30. Mipnets Liverpool 06/03 Conclusions Verification and Testing Group, DCS, University of Sheffield

31. Mipnets Liverpool 06/03 Links Verification and Testing Group, DCS, University of Sheffield