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Scalable agent-based simulations

Greg Goltsov
February 13, 2013

Scalable agent-based simulations

A talk I gave at the end of my Nuffield project a few years back. I've been working on scientifically sound blood clotting simulation with a nice 3d visualisation on top.

Greg Goltsov

February 13, 2013
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  1. Physical modelling of clot formation Xu Z, Lioi J, Mu

    J, Kamocka MM, Liu X, Chen DZ, Rosen ED, & Alber M (2010). A multiscale model of venous thrombus formation with surface-mediated control of blood coagulation cascade. Biophysical journal, 98 (9), 1723-32 PMID: 20441735
  2. Physical modelling of clot formation Xu Z, Lioi J, Mu

    J, Kamocka MM, Liu X, Chen DZ, Rosen ED, & Alber M (2010). A multiscale model of venous thrombus formation with surface-mediated control of blood coagulation cascade. Biophysical journal, 98 (9), 1723-32 PMID: 20441735
  3. Pathology Thromboembolism Formation in a blood vessel of a clot

    (thrombus) that breaks loose and is carried by the blood stream to plug another vessel. Pulmonary embolism Blockage of the main artery of the lung.
  4. Pathology Thromboembolism Formation in a blood vessel of a clot

    (thrombus) that breaks loose and is carried by the blood stream to plug another vessel. Pulmonary embolism Blockage of the main artery of the lung. Aspirin
  5. Aspirin Everyone aged over 45 should consider a small daily

    dose of aspirin to help protect themselves against heart disease and cancer “
  6. Clotting modelling: ODEs Great attention to uid dynamics Not so

    much to internal representation of platelet
  7. Clotting modelling: ODEs Great attention to uid dynamics Not so

    much to internal representation of platelet Probabilistic representation of space
  8. Vs

  9. Clotting modelling: agents Agent-based simulation — platelets are agents. Each

    individual platelet has its own behaviour. Explicit account of space — allows for near-neighbour interactions.
  10. TUNA TECHNOLOGY UNDERPINNING N A N O T E C

    H ASSEMBLERS CoSMoS C O M P L E X S Y S T E M S MODELLING & SIMULATION
  11. TUNA TECHNOLOGY UNDERPINNING N A N O T E C

    H ASSEMBLERS CoSMoS C O M P L E X S Y S T E M S MODELLING & SIMULATION +
  12. TUNA TECHNOLOGY UNDERPINNING N A N O T E C

    H ASSEMBLERS CoSMoS C O M P L E X S Y S T E M S MODELLING & SIMULATION + CrISp CENTRE FOR RESEARCH IN SYSTEMS PATHOLOGY
  13. Hybrid functional Petri net of platelet activation TXA2ext TP receptors

    PLC PIP2 PIP3 IP3R calcium receptor Ca2+ in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc
  14. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  15. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  16. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  17. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  18. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  19. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  20. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  21. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  22. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  23. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  24. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  25. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  26. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc Hybrid functional Petri net of platelet activation
  27. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc
  28. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc
  29. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc
  30. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA
  31. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA
  32. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA COX1
  33. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA COX1
  34. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA TXA2int COX1
  35. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA TXA2int COX1
  36. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA TXA2ext TXA2int COX1
  37. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA TXA2ext TXA2int COX1
  38. TXA2ext TP receptors PLC PIP2 PIP3 IP3R calcium receptor Ca2+

    in cytozole PLA2 PL AA COX-1 PGH2 TXA2int TR1 TR2 TR3 TR4 TR5 TR6 TR7 TR8 TR9 TR10 Aspirin PGTF continuous place continuous transition normal arc test arc inhibitory arc AA TXA2ext TXA2int ASA COX1
  39. COX1 AA TXA2int TR1 TR2 TXA2ext TR4 COX1inact TR3 ASA

    acytCOX1 TR5 Model // Place(name, initial_concentration) NodePtr txa2_ext (new Place("TXA2_ext" NodePtr aa (new Place("AA" NodePtr cox1 (new Place("COX1" NodePtr txa2_int (new Place("TXA2_int" // Transition(name, substrate, product, NodePtr tr1 (new Transition("TR1", tr1_e NodePtr tr2 (new Transition("TR2", tr2_e NodePtr tr3 (new Transition("TR3", tr3_e DSL D O M A I N - S P E C I F I C LANGUAGE
  40. CrISp CENTRE FOR RESEARCH IN SYSTEMS PATHOLOGY { } MODELLING

    SIMULATION VISUALISATION DR UG T EST ING, PHARMACOKINE TICS, PHARMACODYNAMI CS, DRUG D IS TRI BUT ION, DRUG INTER AC TION