System and method for simulating cellular biochemical pathways

• US 7,305,331 B2
• Filed: 02/10/2003
• Issued: 12/04/2007
• Est. Priority Date: 03/10/2000
• Status: Expired due to Fees

• Current Assignee: Industrial Science & Technology Network, Inc.
• Original Assignee: Industrial Science & Technology Network, Inc.
• Inventors: Armstrong, John, Allen, Sandra, Allen, Eric B., Fragoso, Gilberto
• Primary Examiner(s): Moran; Marjorie A
• Application Number:
  US10/360,796
• Publication Number:
  US 20030176978A1
• Time in Patent Office: 1,758 Days
• Field of Search: None
• US Class Current: 703/11
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• 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

Abstract

The present invention relates to a system and method for examining pathways. In particular, the present invention provides a system and method for examining pathways that underlie cellular functions, specifically signal transduction pathways. One aspect of the invention relates to the prediction of (a) functional properties of a protein, (b) potential interaction partners of the protein, and/or (c) potential target biochemical pathways within which the protein may interact. Thus, according to the invention, the influence of a given stimulus on a biochemical pathway can be assessed.

Claims

1. A computer-implemented method for dynamically displaying a animated representation of a biochemical pathway, comprising:

(i) providing as inputs;

(a) a set of separately defined concepts and events, wherein the concepts are capable of joining other concepts,

(b) a physiological context of the biochemical pathway,

(c) at least one stimulus, and

(d) an event corresponding to the at least one stimulus;

(ii) dynamically determining substances available to the biochemical pathway and an order in which events occur in the biochemical pathway; and

(iii) displaying a representation of at least part of the biochemical pathway, wherein the representation is a dynamic animated graphical display.

2. The method of claim 1, wherein the separately defined concepts comprise various attributes.

3. The method of claim 2, wherein the various attributes comprise information on shape, color, size or location of a graphic.

4. The method of claim 1, wherein at least one of the defined concepts comprises a contextual structure.

5. The method of claim 1, wherein at least one of the defined concepts is a compartment within a cell, part or all of an organelle, a cellular membrane, a cytoskeletal structure, a cell, an extracellular fluid, an extracellular structure, a tissue, an organ, or a compartment within an organ.

6. The method of claim 1, wherein at least one of the defined events comprise at least one attribute.

7. The method of claim 6, wherein the at least one attribute comprises reactants, products, inhibitors, and a context within which the at least one of the defined events may occur.

8. The method of claim 6, wherein the at least one attribute comprises information that the at least one of the defined events is inhibited by at least one inhibitor or is inhibited from occurring in at least one location.

9. The method of claim 1, wherein the biochemical pathway comprises a signal transduction pathway.

10. The method of claim 1, wherein the biochemical pathway effects catabolism, anabolism, regulation of oxidative metabolism, regulation of transcription, regulation of protein synthesis, regulation of cell differentiation, or regulation of cell division.

11. The method of claim 1, wherein the biochemical pathway is characteristic of a disease.

12. The method of claim 1, wherein the representation comprises a textual description of objects and processes of at least part of the biochemical pathway, listed in an order in which the objects and processes occur in the pathway.

13. The method of claim 1, wherein the representation comprises a textual description of objects and processes of at least part of the biochemical pathway, listed in a order in which the objects and processes occur in order of time step.

14. The method of claim 1, wherein the representation comprises a graphical representation of objects and processes of at least part of the biochemical pathway, wherein at least one of the objects is represented by a graphic symbol having a combination of color, shape and size unique for the at least one object.

15. The method of claim 14, further comprising displaying at least one textual label that identifies the at least one object that is represented by the graphic symbol.

16. The method of claim 14, further comprising displaying at least one textual label that identifies at least one of the processes.

17. The method of claim 14, further comprising displaying a dynamic animated graphical representation of part or all of the biochemical pathway.

18. The method of claim 1, wherein said concepts are adapted to inherit from other concepts.

19. The method of claim 1, wherein said concepts contain other concepts.

20. The method of claim 1, wherein said concepts comprise attributes.

21. The method of claim 20, wherein said attributes comprise indicia of shape, color, location of a graphic, time, or species.