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(Towards a) Modelling Platform for Biological Systems

(Towards a) Modelling Platform for Biological Systems. Marian Gheorghe University of Sheffield. What the method does. Use computer science models & concepts and software engineering approach & tools Formal model – membrane systems: modular and uses “natural” approach (Nott & Sheff)

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(Towards a) Modelling Platform for Biological Systems

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  1. (Towards a) Modelling Platform for Biological Systems Marian Gheorghe University of Sheffield

  2. What the method does • Use computer science models & concepts and software engineering approach & tools • Formal model – membrane systems: modular and uses “natural” • approach (Nott & Sheff) • Formal analysis + learning mechanisms; • Automated design – structure and parameters • Simulations, verifications, system restructuring and design • FJ Romero-Campero, J Twycross, M Camara, M Bennett, M Gheorghe, N Krasnogor, IJFCS, 2009 • FJ Romero-Campero, N Krasnogor, CiE 2009 • F Bernardini,M Gheorghe,FJ Romero-Campero,N Walkinshaw,WMC 2007

  3. “Natural” modelling -Membrane computing Membranes b a a Objects b a b a c c Regions b Cell Membrane (P) system

  4. What is a (basic) membrane system

  5. Rules and computation • transformation: [a →x]c complex formation/dissociation; activators/inhibitors • communication: a[]c→[a]c, [a]c→ a[]c ; symport, antiport • cell division: [a]c→[b]c [d]c • cell differentiation: [a]c→[b]e • cell death: [a]c→ ; a, b, d, x – multisets • Execution strategies

  6. Modelling molecular interactions

  7. Gene regulatory network - P system model Lac operon in E coli: Hlavacek, Savageau, 1995

  8. Simulations

  9. Invariants of the model Initial values: gene = 1, act = n, rep = m; where n, m either 0 or 10 others = 0 P-invariants PIPE: http://pipe2.sourceforge.net

  10. Property inference

  11. Daikon: Pre-, post-conditions and invariants

  12. Daikon: Pre-, post-conditions and invariants

  13. Daikon: Pre-, post-conditions and invariants 20 !!

  14. Daikon: Pre-, post-conditions and invariants

  15. Formal verification - model checking • Use PRISM – • Probability that the mRNA or the protein is within/under/over some limits • Monotonic increase of some products • Relevant properties • M Kwiatkowska et al 2002

  16. P systems in PRISM P system model PRISM code

  17. Invariants checking – positive regulation … more likely rna’s between 0 and 15, proteins between 0 and 150

  18. Check relationships Relationships between the number of repressors and rna and protein molecules P(prot>rep) P(rna>rep)

  19. Conclusions and further developments

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