Computer-based system and methods for information storage, modeling and simulation of complex systems organized in discrete compartments in time and space

• US 5,930,154 A
• Filed: 07/08/1997
• Issued: 07/27/1999
• Est. Priority Date: 01/17/1995
• Status: Expired due to Fees

• Current Assignee: Intertech Ventures Limited
• Original Assignee: Intertech Ventures Limited
• Inventors: Thalhammer-Reyero, Cristina
• Primary Examiner(s): Kim, Matthew M.
• Assistant Examiner(s): dela Torre, Crescelle N.
• Application Number:
  US08/889,624
• Time in Patent Office: 749 Days
• Field of Search: 345/326, 345/339, 345/348, 345/356, 345/965, 345/969, 345/967, 345/349, 364/188, 364/578
• US Class Current: 703/11
• CPC Class Codes: G05B 17/02 electric
• CPC Class Codes: G16B 5/00 ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/20 Heterogeneous data integration

Abstract

The present invention describes an integrated computer-based system, methods, and graphical interfaces, providing an environment for development and deployment of visual models of complex systems organized in discrete time and space compartments, used for graphic information storage and retrieval, visual modeling and dynamic simulation of said complex systems. In the current implementation the system comprises libraries of knowledge-based building-blocks that include sets of icons representing chemical processes, the pools of entities that participate in those processes, and the graphical description of those entities, encapsulating both information and mathematical models within the modular components, in the form of attributes or in the form of component icons, and a plurality of methods are associated with each of the icons. The models are built by linking each pool to one or several processes, and each process to one or several pools, resulting in complex networks of multidimensional pathways. A number of functions and graphical interfaces can be selected from the menus associated with each icon, to extract in various forms the information contained in the models built with those building blocks. Those functions include the creation of interactive networks of pathways, complex predefined queries based on the relative position of pools of entities in the pathways, the role that the pools play in the processes, the location in compartments, and the structural components of the entities of those pools, and dynamic quantitative simulations. The system integrates inferential control with quantitative and semi-quantitative simulation methods, and provides a variety of alternatives to deal with complex dynamic systems and with incomplete and constantly evolving information and data.

Claims

1. A computer-based system for creating hierarchical virtual-models of dynamic complex-systems, comprising:

libraries of prototypes of building-blocks representing different types of components characteristic of said complex-systems, instances of said prototypes being used to represent components of the complex-system to be modeled, wherein;

certain of said prototypes are simple building-blocks;

certain of said prototypes are composite building-blocks for representing different levels of organizational complexity, each comprising or enabled to comprise any number of instances of building-blocks representing its components;

said simple or composite building-blocks are to be organized within instances of said composite building-blocks in a hierarchy of any number of layers representing organizational compartments or subsystems modeled at different levels of abstraction;

said building-blocks may comprise any number of attributes with values of any type, including but not limited to;

character string, integer or real numbers, logical values, fuzzy values, or instances of images, parameters, variables, lists, arrays, or any other object or data structure, or pointers to instances of any of said building-blocks, external files, Uniform Resource Locators (URLs), database records, or any other objects, in said computer system or in a network accessible by said computer system;

program means for manipulating selected instances of said building-blocks comprising;

means to make said prototypes of building-blocks availaible, including visual means through menus or palettes and/or programmatic means;

means to instantiate said prototypes of building-blocks, including constructor means to create new instances from their definitions and/or means to clone semi-configured instances of said prototypes of building-blocks, interactively and/or programmatically;

means for establishing links between interrelated instances of said building-blocks, directly or through their components; and

means for displaying the components of said composite building-blocks and/or the building-blocks at the other end of said links.

2. A computer-based system as claimed in claim 1, wherein said libraries comprise one or more prototypes of composite time-compartment building-blocks, which instances are used to represent discrete physical or conceptual time intervals characteristic of said complex-systems, each instance capable of holding any number of instances of said building-blocks, including other instances of time-compartment building-blocks, without any limits as to how many layers of lower-level time-compartment building-blocks are built-in to best partition said complex-system into a hierarchy of subsystems.

3. A computer-based system as claimed in claim 2, wherein:

said libraries comprise one or more different prototypes of process building-blocks comprising one or more inputs and/or outputs, each instance of said prototypes to be used to represent a process of said complex-systems with its input(s) and/or output(s), different prototypes representing different types of processes characteristic of said complex-systems;

said instances of process building-blocks of said virtual-models are to be organized within instances of time-compartments of said hierarchy; and

said linking means allow establishing directional links between any of said outputs and inputs of any number of other instances of building-blocks.

4. A computer-based system as claimed in claim 3 further enabling modeling the dynamic quantitative behavior of said virtual-models or their subsystems, further comprising:

one or more different types of quantitative variables associated with corresponding prototypes of building blocks and/or their components, representing characteristics of the components of said complex-systems they represent; and

methods associated with each of said types of variables to dynamically compute the values of instances of said variables comprised in a model during a simulation run.

5. A computer-based system as claimed in claim 2, wherein:

said libraries comprise one or more prototypes of reservoir building-blocks comprising at least one input or one output, each instance of said prototypes to be used to represent a population of any number of units of entities of one given type, or in one given state or compartment, with its input(s) and/or output(s), and wherein each of said population does not need to be physically separated, in a reservoir or otherwise, from other populations of entities in said complex-systems; and

said instances of reservoir building-blocks of said virtual-models are to be organized within said instances of composite building blocks representing an organizational-compartment hierarchy; and

said linking means allow establishing directional links between any of said outputs and inputs of any number of other instances of building-blocks.

6. A computer-based system as claimed in claim 5 further enabling modeling the dynamic quantitative behavior of said virtual-models or their subsystems, further comprising:

one or more different types of quantitative variables associated with said prototypes of reservoir building-blocks and/or their components, and

simulation means, including methods associated with each of said types of variables to dynamically compute the values of any instance of said variables of any instance of corresponding building-block comprised in a model during a simulation run, said values being dependent on the values of any number of variables of other building-blocks linked to input(s) of said instance of building-block.

7. A computer-based system as claimed in claim 5, wherein:

said libraries comprise different prototypes of entity building-blocks, simple or composite, representing different types of entities or entity-components characteristic of said complex-systems, wherein instances of said entity building-blocks are to represent a description of the composition, modular structure, or other characteristics of a representative unit of any of the types of entities that participate in said processes;

said reservoir building-blocks comprise means for any instance to reference the corresponding instance(s) of said entity building-blocks; and

said means further comprise means defined for said reservoir building-blocks to display said referenced instances of entity building-blocks.

8. A computer-based system as claimed in claim 2, wherein:

said libraries comprise one or more prototypes of reservoir building-blocks comprising at least one input or one output, each instance of said reservoir building-blocks to be used to represent a population of any number of units of entities of one given type, or in one given state or compartment, with its input(s) and/or output(s), and wherein each of said populations does not need to be physically separated, in a reservoir or otherwise, from other populations of entities in said complex-systems; and

said instances of reservoir building-blocks of said virtual-models are to be organized within instances of time-compartments of said hierarchy; and

said linking means allow establishing directional links between any of said outputs and inputs of any number of other instances of building-blocks.

9. A computer-based system as claimed in claim 8 further enabling modeling the dynamic quantitative behavior of said virtual-models or their subsystems, further comprising

one or more different types of quantitative variables associated with corresponding prototypes of building-blocks and/or their components representing characteristics of the components of said complex-systems they represent;

and methods associated each of said types of variables to dynamically compute the values of instances of said variables comprised in a model during a simulation run.

10. A computer-based system as claimed in claim 1, wherein:

said libraries comprise one or more different prototypes of process building-blocks comprising one or more inputs and/or outputs, each instance of said prototypes to be used to represent a process of said complex-systems with its input(s) and output(s), different prototypes representing different types of processes characteristic of said complex-systems;

said instances of process building-blocks of said virtual-models are to be organized within said instances of composite building blocks representing an organizational compartment hierarchy; and

said linking means allow establishing directional links between any of said outputs and inputs of any number of other instances of building-blocks.

11. A computer-based system as claimed in claim 10, wherein:

said prototypes of process building-blocks are composite, said inputs and outputs being visual components comprising one or more instances of one or more types of reactant building-blocks representing the one or more inputs to said process as well as the one or more different roles played by said one or more inputs in said process, and one or more instances of product building-blocks representing the one or more outputs from said process; and

said linking means allow to establish links between any of said instances of product building-blocks and reactant building-blocks of any number of said instances of process building-blocks, wherein each instance of reactant building-block may be linked to products of any number of said instances of process building-blocks.

12. A computer-based system as claimed in claim 10, wherein:

said libraries comprise one or more prototypes of reservoir building-blocks comprising at least one input or one output, each instance of said reservoir building-blocks to be used to represent a population of any number of units of entities of one given type, or in one given state or compartment, with its input(s) and/or output(s), wherein each of said inputs and outputs of said process building blocks are to be linked instead to any number of output(s) or input(s), respectively, of said reservoir building-blocks wherein each of said populations does not need to be physically separated, in a reservoir or otherwise, from other populations of entities in said complex-systems; and

said linking means allow establishing links between outputs or inputs of any instance of said reservoir building-blocks and inputs or outputs, respectively, of any number of instances of said process building-blocks.

13. A computer-based system as claimed in claim 12 further enabling modeling the dynamic quantitative behavior of said virtual-models or their subsystems, further comprising:

one or more different types of quantitative variables and/or parameters characteristic of the components of said complex-systems associated with said different prototypes of building-blocks and/or their components, and

simulation means, including means associated with each of said types of variables to dynamically compute the values of instances of said variables of building-blocks comprised in a model selected for a simulation run, said values being dependent on the values of one or more instances of variable of other building-block linked to input(s) of said building-blocks.

14. A computer-based system as claimed in claim 10, wherein:

said libraries comprise different prototypes of entity building-blocks, simple or composite, representing different types of entities or entity-components characteristic of said complex-systems, wherein instances of said entity building-blocks are to represent a description of the composition, modular structure, or other characteristics of a representative unit of any of the types of entities that participate in said processes;

said process building-blocks comprise means for any instance to reference the corresponding instance(s) of said entity building-blocks; and

said means further comprise means defined for said process building-blocks to display said referenced instances of entity building-blocks.

15. A computer system as claimed in claim 10 further enabling modeling the dynamic quantitative behavior of said virtual-models or their subsystems, further comprising:

one or more different types of quantitative variables associated with corresponding prototypes of building blocks representing characteristics of the components of said complex-systems they represent; and

method associated with each of said types of variables to dynamically compute the values of any instance of said variables of any instance of corresponding building-block comprised in a model during a simulation run, said values being dependent on the values of any number of variables of other building-blocks linked to input(s) of said instance of building-block.

16. A computer-based system as claimed in claim 1, wherein said libraries comprise one or more prototypes of composite space-compartment building-blocks, which instances are used to represent discrete physical or conceptual space compartments characteristic of said complex-systems, each instance capable of holding any number of instances of said building-blocks, including other instances of space-compartment building-blocks, without any limits as to how many layers of lower-level space-compartment building-blocks are built-in to best partition said complex-system into a hierarchy of subsystems.

17. A computer-based system as claimed in claim 16, wherein:

said libraries comprise one or more different prototypes of process building-blocks comprising one or more inputs and/or outputs, each instance of said prototypes to be used to represent a process of said complex-systems with its input(s) and output(s), different prototypes representing different types of processes characteristic of said complex-systems;

said instances of process building-blocks of said virtual-models are to be organized within instances of space-compartments at the lowest layers of said hierarchy; and

said linking means allow establishing directional links between any of said outputs and inputs of any number of other instances of building-blocks.

18. A computer-based system as claimed in claim 17 further enabling modeling the dynamic quantitative behavior of said virtual-models or their subsystems, further comprising:

one or more different types of variables and parameters embedded in said building blocks, representing characteristics of the components of said complex-systems they represent; and

methods associated with said types of variables to dynamically compute the values of instances of said variables during simulation runs.

19. A computer-based system as claimed in claim 16, wherein:

said libraries comprise one or more prototypes of reservoir building-blocks comprising at least one input or one output, each instance of said prototypes to be used to represent a population of any number of units of entities of one given type, or in one given state or compartment, with its input(s) and/or output(s), and wherein each of said populations does not need to be physically separated, in a reservoir or otherwise, from other populations of entities in said complex-systems; and

said instances of reservoir building-blocks of said virtual-models are to be organized within instances of space-compartments of said hierarchy; and

said linking means allow establishing directional links between any of said outputs and inputs of any number of other instances of building-blocks.

20. A computer-based system as claimed in claim 19 further enabling modeling the dynamic quantitative behavior of said virtual-models or their subsystems, further comprising

one or more different types of quantitative variables associated with corresponding prototypes of building-blocks and/or their components representing characteristics of the components of said complex-systems they represent;

and methods associated each of said types of variables to dynamically compute the values of instances of said variables comprised in a model during a simulation run.

21. A method for executing hierarchical virtual-models of any complex-system in a computer-system comprising processor means, memory means, storage means, display means, input means, output means, and program means, comprising the steps of:

loading into said memory means it least one stored persistent data set comprising instances of building-blocks representing the components of said complex-system, wherein;

certain of said prototypes are simple building-blocks;

certain of said types of building-blocks are composite, each instance comprising any number of instances of building-blocks representing its components;

said simple or composite building-blocks;

said building-blocks may comprise any number of attributes with any type of values, including but not limited to;

character string, integer or real numbers, logical values, fuzzy values, instances of parameters, variables, lists, arrays, or any other object or data structure, images, or pointers to instances of any of said building-blocks, external files, Uniform Resource Locators (URLs), database records, or any other objects, in said computer system or in a network accessible by said computer system;

executing by said program means for any selected instances of said building-blocks methods providing one or more functions associated with said building-blocks, including show methods defined for composite building-blocks to display the components of the selected instances.

22. A method as claimed in claim 21, wherein said hierarchy of any number of layers include of instances of one or more different types of composite space-compartment building-blocks representing discrete physical or conceptual space compartments of different types or at different levels in a space hierarchy characteristic of said complex-system.

23. A method as claimed in claim 22, wherein the components in said space-compartment hierarchy include any number of instances of one or more different types of process building-blocks with at least one input or one output representing processes characteristic of said complex-systems with their input(s) and/or output(s), and wherein any output of any of said instances is linked to input(s) of any number of other instances of said process building-blocks, further comprising the steps of:

integrating by said program means said linked instances of process building-blocks into a network of multidimensional pathways, wherein any process represented by each node in said network may be comprised in one or more of said pathways, said instances with multiple input links or multiple output links being nodes where different pathways merge or branch, respectively; and

executing by said program means methods to navigate through linked instances of said building-blocks that are downstream and/or upstream of a selected instance in any number of pathways.

24. A method as claimed in claim 23, further enabling dynamic simulations of the quantitative behavior of said virtual-models or their subsystems, wherein quantitative variables and parameters are associated with said instances of building-blocks representing characteristics of the represented components of said complex-systems said program means further comprising simulation means, further comprising the steps of:

requesting a simulation run for any desired combination of one or more interacting pathways, downstream and/or upstream from any one or more selected instances of process building-blocks, and/or for any selected instance(s) of said space-compartment building-blocks;

identifying said program means the set of instances of building-blocks stored in said data set(s) that meet said selected criteria, to be included in said simulation run;

optionally changing the value of any parameters of any of said instances to be included in said simulation run;

controlling the execution of said simulation run; and

dynamically computing by said simulation means the current values over time of said variables for said instances of building-blocks included in said simulation run.

25. A method as claimed in claim 22, wherein the components in said space-compartment hierarchy include any number of instances of one or more different types of reservoir building-blocks with at least one input or one output, each instance representing a population of any number of units of entities of one given type, or in one given state or compartment, with its input(s) and/or output(s), and wherein any output of any of said instances is linked to input(s) of any number of other instances of said reservoir building-blocks, wherein each of said populations of entities does not need to be physically separated in a reservoir or otherwise from other populations of entities in said complex-systems, further comprising the steps of:

integrating by said program means said linked instances of reservoir building-blocks into a network of multidimensional pathways, wherein any reservoir represented by each node in said network may be comprised in one or more of said pathways, said instances with multiple input links or multiple output links being nodes where different pathways merge or branch, respectively; and

executing by said program means methods to navigate through linked instances of said building-blocks that are downstream and/or upstream of any selected instance in any number of pathways.

26. A method as claimed in claim 21, wherein the components in said layers include any number of instances of one or more different types of process building-blocks with at least one input or one output representing processes characteristic of said complex-systems with their input(s) and/or output(s), and wherein any output of any of said instances is linked to input(s) of any number of other instances of said process building-blocks, further comprising the steps of:

integrating by said program means said linked instances of process building-blocks into a network of multidimensional pathways of said interrelated instances, wherein any instance in each node of said network may be comprised in one or more of said pathways, said instances with multiple input links or multiple output links being nodes where different pathways merge or branch, respectively; and

executing by said program means method to navigate through linked instances of said building-blocks that are downstream and/or upstream of a selected instance in any number of pathways.

27. A method as claimed in claim 26, further comprising means for dynamically creating visual displays of said networks of multidimensional pathways representing said complex-systems or their subsystems, further comprising the steps of:

requesting a display of pathways downstream and/or upstream of one or more selected instances of process building-blocks;

identifying by said program means the set of instances of building-blocks stored in said data set(s) that meet said selected criteria, to be represented by the nodes of the network of pathways in said displays;

creating by said program means visual representations of said identified stored instances of process building-blocks; and

a dynamically generating a layout on said display means with said visual representations connected as the nodes of a network of one or more pathways, wherein said connectors extended between said visual nodes are directed to indicate a directional relationship.

28. A method-based as claimed in claim 26, wherein:

said instances of process building-blocks are composite and said inputs and outputs are visual components comprising one or more instances of one or more types of reactant building-blocks representing the one or more inputs and the one or more different roles they play in said process, and one or more instances of product building-blocks representing the one or more outputs from said process;

any instance of said product building-blocks of any process building-block is linked to instance(s) of reactant building-blocks of any number of other instances of process building-blocks each instance of reactant building-block being linked to instance(s) of product building-blocks of any number of other instances of process building-blocks; and

said instances of process building-blocks are dynamically integrated by said program means into said network of multidimensional pathways based on said links between product and reactant building-block.

29. A method as claimed in claim 26, wherein:

the components in said layers further comprise any number of instances of one or more different types of reservoir building-blocks with at least one input or one output, each instance representing a population of any number of units of entities of one given type, or in one given state or compartment, with its input(s) and/or output(s), wherein each of said populations of entities does not need to be physically separated in a reservoir or otherwise from other populations of entities in said complex-systems;

any output of any of said instances of process building-block is linked to an input of one instance of reservoir building-block and any input of any instance of process building-blocks is linked to an output of one instance of reservoir building-blocks;

said program means integrate said alternating linked instances of reservoir and process building-blocks into said network of multidimensional pathways; and

executing by said program means for any of selected instances of reservoir or process building-blocks said one or more methods defined said linked instances of building-blocks may include either one or both of said types of building-blocks, such as said show methods display the linked instance of the complementary building-blocks, or said list methods create lists of said instances of linked reservoir or process building-blocks that are downstream or upstream, in any number of pathways, of a selected instance of reservoir or process building-block.

30. A method as claimed in claim 29, further enabling dynamic simulations of the quantitative behavior of said virtual-models or their subsystems, wherein quantitative variables and parameters are associated with said instances of building-blocks of said virtual models representing characteristics of the represented components of said complex-systems, said program means further comprising simulation means, further comprising the steps of:

requesting a simulation run for any desired combination of one or more interacting pathways, downstream and/or upstream, from any one or more selected instances of reservoir building-blocks, and/or for any selected instance(s) of composite building-blocks of said hierarchy of any number of layers;

identifying by said program means the set of instances of building-blocks stored in said data sets that meet said selected criteria, to be included in said simulation run;

optionally changing the value of any parameters of any of said instances of building-blocks to be included in said simulation run;

using said simulation means for controlling said simulation; and

dynamically computing by said simulation means the current values over time of said variables for said instances of building-blocks included in said simulation run.

31. A method as claimed in claim 29, further comprising means for dynamically creating visual displays of said networks of multidimensional pathways representing said complex-systems or their subsystems, further comprising the steps of:

requesting a display of pathways of reservoir and/or process building-blocks downstream and/or upstream of one or more selected instances of reservoir or process building-blocks with a scope comprising one or more selected space-compartment building-blocks;

identifying by said program means the set of instances of building-blocks stored in said data set(s) that meet said selected criteria, to be represented by the nodes of the network of pathways in said displays;

creating by said program means visual representations of said identified stored instances of reservoir and/or process building-blocks; and

dynamically generating a layout on said display means with said visual representations connected as the nodes of a network of one or more pathways, wherein said connectors extended between said visual nodes are directed to indicate a directional relationship.

32. A method as claimed in claim 26, wherein said data set(s) further comprise instances of composite entity building-blocks representing descriptions of the composition, modular structure, or other characteristics of a representative unit of any of the types of entities that participate in said processes, which may have references to their corresponding instances of said entity building-blocks, further comprising the steps of:

executing by said program means for any selected instance of said composite entity building-blocks the show methods defined for said building-blocks to display their components representing different types of entity-components characteristic of said entities, without any limits as to how many layers of lower-level composite entity building-blocks are built into any composite entity building-block; and

executing by said program means for any selected instances of process building-blocks with said references the show methods defined for said building-blocks to display their corresponding instances of entity building-blocks.

33. A method as claimed in claim 26, further enabling dynamic simulations of the quantitative behavior of said virtual-models or their subsystems, wherein quantitative variables and parameters are associated with said instances of building-blocks representing characteristics of the represented components of said complex-systems, said program means further comprising simulation means, further comprising the steps of:

requesting a simulation run for any desired combination of one or more interacting pathways downstream and/or upstream from any one or more selected instances of process building-blocks, and/or for any selected instance(s) of composite building-blocks of said hierarchy of any number of layers;

identifying by said program means the set of instances of building-blocks stored in said data set(s) that meet the selected criteria, to be included in said simulation run;

optionally changing the value of any parameters of any of said instances building-blocks to be included in said simulation run;

controlling the execution of said simulation run; and

dynamically computing by said simulation means the current values over time of said variables for said instances of building-blocks included in said simulation run.

34. A method as claimed in claim 21, wherein the components in said layers include any number of instances of one or more different types of reservoir building-blocks with at least one input or one output, each instance representing a population of any number of units of entities of one given type, or in one given state or compartment, with its input(s) and/or output(s), and wherein any output of any of said instances is linked to input(s) of any number of other instances of said reservoir building-blocks, wherein each of said populations of entities does not need to be physically separated in a reservoir or otherwise from other populations of entities in said complex-systems, further comprising the steps of:

integrating by said program means said linked instances of reservoir building-blocks into a network of multidimensional pathways, wherein any reservoir represented by each node in said network may be comprised in one or more of said pathways, said instances with multiple input links or multiple output links being nodes where different pathways merge or branch, respectively; and

executing by said program means methods to navigate through linked instances of said building-blocks that arc downstream and/or upstream of any selected instance in any number of pathways.

35. A method as claimed in claim 34, further enabling dynamic simulations of the quantitative behavior of said virtual-models or their subsystems, wherein variables and parameters are associated with said instances of building-blocks of said virtual models representing characteristics of the represented components of said complex-systems, said program means further comprising simulation means, further comprising the steps of:

requesting a simulation run for any desired combination of one or more interacting pathways, downstream and/or upstream from any one or more selected instances of reservoir building-blocks, and/or for any selected instance(s) of composite building-blocks of said hierarchy of any number of layers;

identifying by said program means the set of instances of building-blocks stored in said data set(s) that meet said selected criteria, to be included in said simulation run;

optionally changing the value of any parameters of any of said instances of building-blocks to be included in said simulation run;

controlling the execution of said simulation run; and

dynamically computing by said simulation means the current values over time of said variables for said instances of building-blocks included in said simulation run.

36. A method as claimed in claim 34, further comprising means for dynamically creating visual displays of networks of connected multidimensional pathways representing said complex-systems or their subsystems, further comprising the steps of:

requesting a display of pathways downstream and/or upstream of one or more selected instances of reservoir building-blocks;

identifying by said program means the set of instances of building-blocks stored in said data set(s) that meet said selected criteria, to be represented by the nodes of the pathways in said displays;

creating by said program means visual representations of said identified stored instances of building-blocks; and

dynamically generating a layout on said display means with said visual representations connected as the nodes of a network of one or more pathways, wherein said connectors extended between said visual nodes are directed to indicate a directional relationship.

37. A method as claimed in claim 34, wherein said data set(s) further comprise instances of composite entity building-blocks representing descriptions of the composition, modular structure, or other characteristics of representative units of any of the populations of entities represented by said instances of reservoir building-blocks, which may have references to their corresponding instances of said entity building-blocks, further comprising the steps of:

executing by said program means for any selected instance of said composite entity building-blocks the show methods defined for said building-blocks to display their components representing different types of entity-components characteristic of said entities, without any limits as to how many layers of lower-level composite entity building-blocks are built into any composite entity building-block; and

executing by said program means for any selected instances of reservoir building-blocks with said references the show methods defined for said building-blocks to display their corresponding instances of entity building-blocks.

38. A method as claimed in claim 21, wherein said hierarchy of any number of layers include instances of one or more different types of composite time-compartment building-blocks representing discrete physical or conceptual time intervals of different types or at different levels in a time interval hierarchy characteristic of said complex-system.

39. A method as claimed in claim 38, wherein the components in said time-compartments hierarchy include any number of instances of one or more different types of process building-blocks with at least one input or one output representing processes characteristic of said complex-systems with their input(s) and/or output(s), and wherein any output of any of said instances is linked to input(s) of any number of other instances of said process building-blocks, further comprising the steps of:

integrating by said program means said linked instances of process building-blocks into a network of multidimensional pathways, wherein any process represented by each node in said network may be comprised in one or more of said pathways, said instances with multiple input links or multiple output links being nodes where different pathways merge or branch, respectively; and

executing by said program means methods to navigate through linked instances of said process building-blocks that are downstream and/or upstream of a selected instance in any number of pathways.

40. A method as claimed in claim 39, further enabling dynamic simulations of the quantitative behavior of said virtual-models or their subsystems, wherein quantitative variables and parameters are associated with said instances of building-blocks representing characteristics of the represented components of said complex-systems, said program means further comprising simulation means, further comprising the steps of:

requesting a simulation run for any desired combination of one or more interacting pathways, downstream and/or upstream from any one or more selected instances of process building-blocks, and/or for any selected instance(s) of said time-compartment building-blocks;

identifying by said program means the set of instances of building-blocks stored in said data set(s) that meet said the selected criteria, to be included in said simulation run;

optionally changing the value of any parameters of any of said instances to be included in said simulation run;

controlling the execution of said simulation run; and

dynamically computing by said simulation means the current values over time of said variables for said instances of building-blocks included in said simulation run.

41. A method as claimed in claim 38, wherein the components in said time-compartment hierarchy include any number of instances of one or more different types of reservoir building-blocks with at least one input or one output, each instance representing a population of any number of units of entities of one given type, or in one given state or compartment, with its input(s) and/or output(s), and wherein any output of any of said instances is linked to input(s) of any number of other instances of said reservoir building-blocks, wherein each of said populations of entities does not need to be physically separated in a reservoir or otherwise from other populations of entities in said complex-systems, further comprising the steps of;

integrating by said program means said linked instances of reservoir building-blocks into a network of multidimensional pathways, wherein any reservoir represented by each node in said network may be comprised in one or more of said pathways, said instances with multiple input links or multiple output links being nodes where different pathways merge or branch, respectively; and

executing by said program methods to navigate through linked instances of said building-blocks that are downstream and/or upstream of any selected instance in any number of pathways.

42. A computer system for modeling dynamic complex biological systems at different levels of organizational complexity, comprising:

a hierarchy of one or more levels of components representing different levels of biological complexity, any of said levels comprising any number of components including;

components each comprising any number of further levels of components, and

linkable components of one or more different types representing interrelated components characteristic of the corresponding level of complexity of said biological systems, including one or more different types of components representing various types of biological processes; and

program means for creating and/or manipulating executable models of said complex biological systems based on said one or more levels and their linkable components.

43. A computer system as claimed in claim 42, wherein any of said linkable components is linked to any number of other linkable components in the same level or in different levels.

44. A computer system as claimed in claim 42, wherein said linkable components further comprise any number of interrelated variables characteristic of the biological components they represent for modeling the dynamic behaviour of said complex biological system.

45. A computer system as claimed in claim 42, wherein said linkable components further include one or more different types of components representing various populations of entities that participate in said biological processes as inputs and/or outputs, each of said populations comprising biological or chemical entities of any one given type, or any one given state or compartment, characteristic of the corresponding level of complexity.

46. A computer system as claimed in claim 42, wherein any of said linkable components representing one of said populations of entities is linked to any number of said linkable components representing biological processes which provide inputs to or receive outputs from said population.

47. A computer system as claimed in claim 42, wherein said program means include means for navigating through the information provided by said one or more levels and their linkable components.

48. A computer system as claimed in claim 42, wherein said program means include means for synthesizing and presenting to users new information from the information provided in said one or more levels of linkable components.