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1. (WO2017004607) ENVIRONNEMENT DE SIMULATION POUR UNE CONCEPTION EXPÉRIMENTALE
Note: Texte fondé sur des processus automatiques de reconnaissance optique de caractères. Seule la version PDF a une valeur juridique

CLAIMS

What is claimed is:

1. A method for enabling a simulation environment for experimental design, the method comprising:

receiving a request to initiate a simulation of a biological model, wherein the request comprises a selection of initial molecule types, wherein each molecule type describes one or more interaction points, wherein each interaction point describes an input and an outcome of a biological event;

instantiating a virtual 3-D geometric space with a collection of virtual molecules from the selection of initial molecule types, wherein each of the virtual molecules comprises an initial state;

sending a periodic iteration command to the collection of virtual molecules, wherein each periodic iteration command demarks the beginning of a new action cycle;

in response to receiving the periodic iteration command, each of the virtual molecules:

processes a received set of broadcast messages, wherein a broadcast message in the received set describes a contact with an interaction point of a neighboring virtual molecule;

determines and performs one or more behaviors in accordance with the processed broadcast messages; and

waits for a next periodic iteration command.

2. The method of claim 1, wherein the one or more behaviors are selected from a group consisting of:

in response to a determined interaction point reaction, one or more of:

transforming the molecule type of the virtual molecule,

adding a new virtual molecule, and

removing another virtual molecule from the virtual 3-D geometric space; modifying a velocity or vector of motion of the virtual molecule within the virtual 3-D geometric space;

sending an outbound broadcast message describing a particular biological event;

modifying one or more parameter of the virtual molecule; and

taking no action.

3. The method of claim 2, wherein the particular biological event is selected from a group consisting of activation, deactivation, binding, releasing, transforming, methylation, phosphorylation, ubiquitination, N-methylation, O-glycosylation, N-glycosylation, misfolding, truncation, degradation, and biological/chemical modifications affecting the secondary, tertiary, or quaternary structure of a molecule.

4. The method of claim 1, further comprising storing, in a data store, a current state of the simulation of the biological model for the new action cycle.

5. The method of claim 4, wherein the current state of the simulation of the biological model comprises activity data for each virtual molecule for each action cycle.

6. The method of claim 5, wherein the activity data comprises one or more of:

a representation of the received set of broadcast messages;

one or more current parameter; and

a representation of the one or more behaviors.

7. The method of claim 1, wherein the initial state comprises one or more of a mass, a number of copies of the virtual molecule, a random initial position within the virtual 3-D geometric space, and a random initial velocity.

8. The method of claim 1, wherein the biological model is a model of a neuron.

9. The method of claim 1, wherein the biological model is a virtual test tube.

10. The method of claim 1, wherein the selection of initial molecule types comprises one or more of an organelle having one or more molecule types, an experimental molecule type, and a molecule type selected from a repository.

11. The method of claim 1, wherein one of the one or more interaction points comprises a proposed interaction point.

12. A system for enabling a simulation environment for experimental design, the system comprising:

program instructions stored on one or more computer readable storage media for a controller service that, when executed by a processing system, direct the processing system to:

in response to receiving a request to initiate a simulation of a biological model, wherein the request comprises a selection of initial molecule types, wherein each molecule type describes one or more interaction points, wherein each interaction point describes an input and an outcome of a biological event:

instantiate a virtual three-dimensional (3-D) geometric space with a collection of virtual molecules from the selection of initial molecule types, wherein each of the virtual molecules comprises an initial state;

divide the virtual 3-D geometric space into one or more geometric portions sized in accordance with available work nodes;

distribute the one or more geometric portions to the available work nodes for processing, wherein each geometric portion comprises a subset of the plurality of virtual molecules;

send a periodic iteration command to a processing work node, wherein each periodic iteration command demarks the beginning of a new action cycle; and

one or more work nodes, each work node having second program instructions stored on second one or more computer readable storage media that, when executed by second processing system, direct the processing system to:

in response to receiving the periodic iteration command, instruct each virtual molecule in the subset of the plurality of virtual molecules to:

process a received set of broadcast messages, wherein a broadcast message in the received set describes a contact with an interaction point of a neighboring virtual molecule;

determine and perform one or more behaviors in accordance with the processed broadcast messages; and

store, in a data store, activity data for the virtual molecule for the new action cycle.

13. The system of claim 12, wherein the controller service further comprises program instructions that, when executed by the processing system, direct the processing system to: in response to receiving an indication of a focus area of the biological model, wherein the focus area is defined by spatial coordinates within the a virtual 3-D geometric space and by temporal coordinates:

access the data store to obtain a focus area state of the focus area of the biological model; and

provide the focus area state.

14. The system of claim 12, wherein the one or more behaviors are selected from a group consisting of:

in response to a determined interaction point reaction, one or more of:

transforming the molecule type of the virtual molecule,

adding a new virtual molecule, and

removing another virtual molecule from the virtual 3-D geometric space;

modifying a velocity or vector of motion of the virtual molecule within the virtual 3-D geometric space;

sending an outbound broadcast message describing a particular biological event;

modifying one or more parameter of the virtual molecule; and

taking no action.

15. The system of claim 14, wherein the particular biological event is selected from a group consisting of activation, deactivation, binding, releasing, transforming, methylation, phosphorylation, ubiquitination, N-methylation, O-glycosylation, N-glycosylation, misfolding, truncation, degradation, and biological/chemical modifications affecting the secondary, tertiary, and quaternary structure of a molecule.

16. The system of claim 12, wherein a current state of the simulation of the biological model comprises the activity data for each virtual molecule for each action cycle.

17. The system of claim 16, wherein the activity data comprises one or more of: a representation of the received set of broadcast messages;

one or more current parameter; and

a representation of the one or more behaviors.

18. The system of claim 12, wherein the initial state comprises one or more of a mass, a number of copies of the virtual molecule, a random initial position within the virtual 3-D geometric space, and a random initial velocity.

19. The system of claim 12, wherein the biological model is a model of a neuron.

20. The system of claim 12, wherein the biological model is a virtual test tube.

21. The system of claim 12, wherein the selection of initial molecule types comprises one or more of an organelle having one or more molecule types, an experimental molecule type, and a molecule type selected from a repository.

22. The system of claim 12, wherein one of the one or more interaction points comprises a proposed interaction point.

23. The method of any one of claims 1 to 11, wherein the virtual 3-D geometric space is rendered to a display.

24. The method of any one of claims 1 to 11, wherein the request to initiate the simulation is received via a processing system.

25. The system of any one of claims 12 to 22, wherein the virtual 3-D geometric space is rendered to a display.

26. The system of any one of claims 12 to 22, wherein the request to initiate the simulation is received via a processing system.

27. A method for enabling a simulation environment for experimental design, the method comprising:

receiving a request to initiate a simulation of a biological model of a cell having organelles (cell model), wherein the request comprises a selection of initial entities comprising one or more organelles of the cell model and one or more molecule types contained within, or associated with the one or more organelles of the cell model, wherein each entity has one or more interaction points, and wherein each interaction point describes an input and an outcome of a biological event;

instantiating the initial entities of the request to a data structure representing a virtual three-dimensional (3-D) geometric space, wherein the instantiated data structure comprises the selection of initial entities at locations within the virtual 3-D geometric space, wherein the instantiated data structure describes an initial state of each instantiated entity and describes a plurality of available behaviors for each instantiated entity, and wherein one or more of the available behaviors is to be determined and performed upon an interaction event;

performing a periodic iteration to evaluate each interaction point of each instantiated entity within the virtual 3-D geometric space to identify interactions with other instantiated entities that would result in performance of a determined behavior, wherein each periodic iteration command demarks the beginning of a new action cycle;

wherein, in the periodic iteration, each of the instantiated entities:

updates its position and velocity within the virtual 3-D geometric space;

identifies occurrence of a collision, if present, with other instantiated entities and performs one or more determined behaviors from among the plurality of available behaviors, wherein the plurality of available behaviors includes, at least each of: binding or releasing of an instantiated entity, changing the secondary, tertiary, or quaternary structure of an instantiated entity, and transforming an instantiated entity to a different entity type;

performs the determined one or more behaviors; and

waits for a next periodic iteration command.

28. The method of claim 27, wherein the plurality of available behaviors further includes, at least each of:

adding a new instantiated entity to the virtual 3-D geometric space,

removing one or more of the instantiated entities from the virtual 3-D geometric space,

modifying a velocity or vector of motion of one or more of the instantiated entities within the virtual 3-D geometric space, and

modifying one or more parameters of one or more of the instantiated entities.

29. The method of claim 28, wherein the biological event is selected from the group consisting of activation, deactivation, binding, releasing, transforming, methylation, phosphorylation, ubiquitination, N-methylation, O-glycosylation, N-glycosylation, misfolding, truncation, degradation, and biological/chemical modifications affecting the secondary, tertiary, or quaternary structure of a molecule.

30. The method of claim 27, further comprising storing, in a data store, a current state of the simulation of the cell model for the new action cycle.

31. The method of claim 30, wherein the current state of the simulation of the cell model comprises activity data for each instantiated entity for each action cycle.

32. The method of claim 31, wherein the activity data comprises one or more of: one or more current parameters; and

a representation of the one or more behaviors.

33. The method of claim 27, wherein the initial state of each instantiated entity comprises one or more of a mass of the instantiated entity, a number of copies of the instantiated entity, a random initial position of each instantiated instance of the entity within the virtual 3-D geometric space, and a random initial velocity of each instance of the instantiated entity.

34. The method of claim 27, wherein the cell model is a neuron model.

35. The method of claim 27, wherein the selection of initial entities comprises at least one experimental molecule type, or at least one molecule type selected from a repository, or both.

36. The method of claim 27, wherein one of the one or more interaction points comprises a proposed interaction point.

37. A system for enabling a simulation environment for experimental design, the system comprising:

program instructions stored on one or more non-transitory computer readable storage media for a controller service that, when executed by a processing system, direct the processing system to:

in response to receiving a request to initiate a simulation of a biological model of a cell having organelles (cell model), wherein the request comprises a selection of initial entities comprising one or more organelles of the cell model and one or more molecule types contained within, or associated with the one or more organelles of the cell model, wherein each entity has one or more interaction points, and wherein each interaction point describes an input and an outcome of a biological event:

instantiate the initial entities of the request to a data structure representing a virtual three-dimensional (3-D) geometric space, wherein the instantiated data structure comprises the selection of initial entities at locations within the virtual 3-D geometric space, wherein the instantiated data structure describes an initial state of each instantiated entity and describes a plurality of available behaviors for each instantiated entity, and wherein one or more of the available behaviors is to be determined and performed upon an interaction event;

divide the virtual 3-D geometric space into one or more geometric portions sized in accordance with available work nodes;

distribute the one or more geometric portions to the available work nodes for processing, wherein each geometric portion comprises a subset of the instantiated entities;

send a periodic iteration command to a processing work node, wherein each periodic iteration command demarks the beginning of a new action cycle; and

one or more work nodes, each work node having second program instructions stored on second one or more computer readable storage media that, when executed by second processing system, direct the processing system to:

in response to receiving the periodic iteration command, instruct each instantiated entity in the subset of instantiated entities to:

update the instructed instantiated entity's position and velocity within the virtual 3-D geometric space,

identify occurrence of a collision, if present, with other instantiated entities and perform one or more determined behaviors from among the plurality of available behaviors, wherein the plurality of available behaviors includes, at least each of: binding or releasing of an instantiated entity, changing the secondary, tertiary, or quaternary structure of an instantiated entity, and transforming an instantiated entity to a different entity type;

store, in a data store, activity data for the instantiated entity for the new action cycle.

38. The system of claim 37, wherein the controller service further comprises program instructions that, when executed by the processing system, direct the processing system to: in response to receiving an indication of a focus area of the cell model, wherein the focus area is defined by spatial coordinates within the virtual 3-D geometric space and by temporal coordinates:

access the data store to obtain a focus area state of the focus area of the cell model; and

provide the focus area state.

39. The system of claim 37, wherein the plurality of available behaviors further includes, at least each of:

adding a new instantiated entity to the virtual 3-D geometric space, and

removing one or more of the instantiated entities from the virtual 3-D geometric space,

modifying a velocity or vector of motion of one or more of the instantiated entities within the virtual 3-D geometric space, and

modifying one or more parameters of one or more of the instantiated entities.

40. The system of claim 39, wherein the biological event is selected from the group consisting of activation, deactivation, binding, releasing, transforming, methylation, phosphorylation, ubiquitination, N-methylation, O-glycosylation, N-glycosylation, misfolding, truncation, degradation, and biological/chemical modifications affecting the secondary, tertiary, and quaternary structure of a molecule.

41. The system of claim 37, wherein a current state of the simulation of the cell model comprises the activity data for each instantiated entity for each action cycle.

42. The system of claim 41, wherein the activity data comprises one or more of: one or more current parameters; and

a representation of the one or more behaviors.

43. The system of claim 37, wherein the initial state of each instantiated entity comprises one or more of a mass of the instantiated entity, a number of copies of the instantiated entity, a random initial position of the instantiated entity within the virtual 3-D geometric space, and a random initial velocity of the instantiated entity.

44. The system of claim 37, wherein the cell model is a model of a neuron.

45. The system of claim 37, wherein the selection of initial entities comprises at least one experimental molecule type, or at least one molecule type selected from a repository, or both.

46. The system of claim 37, wherein one of the one or more interaction points comprises a proposed interaction point.

47. The method of any one of claims 27 to 36, wherein the virtual 3-D geometric space is rendered to a display.

48. The method of any one of claims 27 to 36, wherein the request to initiate the simulation is received via a processing system.

49. The system of any one of claims 37 to 46, wherein the virtual 3-D geometric space is rendered to a display.

50. The system of any one of claims 37 to 46, wherein the request to initiate the simulation is received via a processing system.