Network models of complex systems

A method of creating a computer-implemented model for modeling a dynamic multi-variable biological system, wherein the biological system is controlled by a plurality of interrelated biologic processes defining functions occurring within the biological system, comprising:

• a) creating a first class of objects representing state variables holding a scalar real number value, wherein the set of values of all first class objects in a simulation model defines the state of the model at a certain point in time;
• b) creating a second class of objects representing processes in the simulation model that result in changes in the values of one or more first class objects, wherein the way of change of the values of the first class objects can be either discrete or continuous;
• c) establishing references between certain of said first class objects and certain of said second class of objects, to indicate which second class of objects affect changes in which first class objects in the simulation model;
• d) implementing equation solvers of one or more type;
• and
• e) executing said dynamic model by applying said equation solvers to change the values of said first class objects.

A method of interactively or dynamically generating by a computer program a display, on a display device, of a complex biological system model built using a plurality of reusable discrete components, each conforming to an interface specification, wherein one or more of said discrete components is a composite component, the method comprising:

• a) displaying a set of reusable respective node representations for the plurality of discrete components;
• b) displaying a set of reusable respective link representations for the plurality of relationships between the plurality of discrete components, such as cause-effect, conversion, association, or translocation relationships;
• c) determining user or program selection of a number of said node representations;
• and
• d) determining user or program selection of a number of said link representations to represent the relationships between said selected node representations;
• and
• e) displaying the linked representation of the selected corresponding node and link representation instances to represent the relationships between the plurality of instances of the discrete components.

A method for generating a model of a complex biological system in a computer system, the computer system comprising:

• i) one or more defined classes of typed symbols representing different elements of the complex biological system,
• ii) one or more defined classes of typed relations between at least two of the symbols for expressing the corresponding one or more types of relationships between at least two of the elements, including one or more relationships selected from the group of downstream, upstream, composition, linkage, association, regulation and containment relationships;
• iii) one or more defined rules or procedures comprising an operator for establishing one or more of said typed relations between at least two symbols;
• iii) one or more defined inference rules comprising an operator to reason about said symbols and their relations, the rules being expressed in a manner that enables use by an inference engine;
• and
• the method comprising the steps of:
• a) applying said one or more rules or procedures for establishing said typed relations between at least one symbol to at least another symbol;
• b) using the inference engine to infer alternative results from the system based on at least some of said symbols and their relations, given an initial hypothetical state or set of conditions.

A method for generating (recording) computable knowledge in a complex domain, to facilitate the computerized analysis and integration of the large amount of knowledge in such domain, comprising:

• a) defining a hierarchy of different classes of domain-specific typed symbols representing an ontology of the different elements and concepts of the complex domain, wherein at least some general knowledge about the pertinent elements and concepts in such domain is incorporated in the definitions of said typed symbols;
• b) defining one or more classes of typed relations between at least two of the classes of typed symbols for expressing the corresponding one or more types of relationships between at least two of the elements and concepts in the complex domain, including one or more relationships selected from the group of downstream, upstream, composition, linkage, association, regulation and containment relationships;
• c) defining one or more rules or procedures comprising an operator for establishing one or more of said defined typed relations between at least two typed symbols;
• d) applying said one or more rules or procedures for establishing said typed relations between at least one symbol to at least another symbol;
• and
• e) defining one or more rules or procedures comprising an operator to traverse the network formed by said symbols and their relations, thereby making the knowledge contained in said network available for further computations.