SPLIT, BREAK, SUBSTITUTE, AND FRAGMENT-SPLICE OPERATIONS FOR COMPUTER MODELS OF ENZYME CASCADES, METABOLIC SIGNAL TRANSDUCTION, SIGNALING PATHWAYS, CATALYTIC CHEMICAL REACTION NETWORKS, AND IMMUNOLOGY

• US 20140129196A1
• Filed: 01/08/2014
• Published: 05/08/2014
• Est. Priority Date: 04/26/2009
• Status: Abandoned Application

• Current Assignee: NRI R&D Patent Licensing, LLC (Advanced Touchscreen and Gesture Technologies, LLC)
• Original Assignee: NRI R&D Patent Licensing, LLC (Advanced Touchscreen and Gesture Technologies, LLC)
• Inventors: Ludwig, Lester F.
• Application Number:
  US14/150,010
• Publication Number:
  US 20140129196A1
• Time in Patent Office: Days
• US Class Current: 703/2
• CPC Class Codes: G06F 17/16 Matrix or vector computation , e.g. matrix-matrix or matrix-vector multiplication, matrix factorization matrix transposition G06F7/78
• CPC Class Codes: G06F 7/60 Methods or arrangements for performing computations using a digital non-denominational number representation, i.e. number representation without radix; Computing devices using combinations of denominational and non-denominational quantity representations , e.g. using difunction pulse trains, STEELE computers, phase computers conversion of digital data to or from non-denominational form H03M5/00, H03M7/00
• 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

Computer utilities for adapting data and properties of computer modeled biochemical pathways for use in a modified form. Utilities can be provided for split, break, substitute, and fragment-splice operations are presented for computer models of enzyme cascades, metabolic signal transduction, signaling pathways, catalytic chemical reaction networks, and immunology. Substitution operations can be used in situations where a specific portion of a modeled biochemical pathway is identified and replaced with an alternate topologically-compatible portion of a modeled biochemical pathway. Split/break operations can be used to break a modeled biochemical pathway into two or more fragments. Splice operations can be used to splice fragments obtained from previous editing operations. These and other operations can be used to introduce a new node or pathway hop in a step in a modeled biochemical pathway. The invention provides for resultant modeled biochemical pathway to comprise added feedback, feedforward, allosteric and/or non-allosteric modulation attributes and components.

Claims

1. A computer utility for adapting data and properties of a computer modeled biochemical pathway for use in a modified form, the computer utility comprising:

an interactive user interface;

a stored computer model of a biochemical pathway;

a pathway editing component controlled by the user interface for editing the stored computer model of the biochemical pathway;

wherein the interactive user interface is used to select the stored computer model of the biochemical pathway for editing, and

wherein the pathway editing component is configured to introduce a substitution in at least one portion of the computer model of the biochemical pathway so as to create a modified biochemical pathway computer model.

2. The computer utility of claim 1 wherein the substitution operation used to introduce a new node in the modeled biochemical pathway.

3. The computer utility of claim 1 wherein the substitution operation used to introduce a pathway hop in the modeled biochemical pathway.

4. The computer utility of claim 1 wherein the substitution operation used to add a feedback path in the modeled biochemical pathway.

5. The computer utility of claim 1 wherein the substitution operation used to add a feedforward path in the modeled biochemical pathway.

6. The computer utility of claim 1 wherein the substitution operation used to add an allosteric modulation in the modeled biochemical pathway.

7. The computer utility of claim 1 wherein the substitution operation used to add a non-allosteric modulation in the modeled biochemical pathway.

8. A computer utility for adapting data and properties of a computer modeled biochemical pathway for use in a modified form, the computer utility comprising:

an interactive user interface;

a stored computer model of a biochemical pathway;

a pathway editing component controlled by the user interface for editing the stored computer model of the biochemical pathway;

wherein the interactive user interface is used to select the stored computer model of the biochemical pathway for editing, and

wherein the pathway editing component is configured to split the computer model of the biochemical pathway into at least two fragments.

9. The computer utility of claim 8 wherein the split operation used to introduce a new node in the modeled biochemical pathway.

10. The computer utility of claim 8 wherein the split operation used to introduce a pathway hop in the modeled biochemical pathway.

11. The computer utility of claim 8 wherein the split operation used to add an allosteric modulation in the modeled biochemical pathway.

12. The computer utility of claim 8 wherein the split operation used to add a non-allosteric modulation in the modeled biochemical pathway.

13. A computer utility for adapting data and properties of a computer modeled biochemical pathway for use in a modified form, the computer utility comprising:

an interactive user interface;

a stored computer model of a biochemical pathway;

a pathway editing component controlled by the user interface for editing the stored computer model of the biochemical pathway;

wherein the interactive user interface is used to select the stored computer model of the biochemical pathway for editing, and

wherein the pathway editing component is configured to break the computer model of the biochemical pathway into at least two fragments.

14. The computer utility of claim 13 wherein the break operation used to introduce a new node in the modeled biochemical pathway.

15. The computer utility of claim 13 wherein the break operation used to introduce a pathway hop in the modeled biochemical pathway.

16. The computer utility of claim 13 wherein the break operation used to add an allosteric modulation in the modeled biochemical pathway.

17. The computer utility of claim 13 wherein the break operation used to add a non-allosteric modulation in the modeled biochemical pathway.

18. A computer utility for adapting data and properties of a computer modeled biochemical pathway for use in a modified form, the computer utility comprising:

an interactive user interface;

a stored computer model of a biochemical pathway;

a pathway editing component controlled by the user interface for editing the stored computer model of the biochemical pathway;

wherein the interactive user interface is used to select the stored computer model of the biochemical pathway for editing, and

wherein the pathway editing component is configured to splice at least two fragments of computer models of the biochemical pathway, the fragments obtained from previous editing operations.

19. The computer utility of claim 18 wherein the splice operation used to introduce a new node in the modeled biochemical pathway.

20. The computer utility of claim 18 wherein the splice operation used to introduce a pathway hop in the modeled biochemical pathway.

21. The computer utility of claim 18 wherein the splice operation used to add a feedback path in the modeled biochemical pathway.

22. The computer utility of claim 18 wherein the splice operation used to add a feedforward path in the modeled biochemical pathway.

23. The computer utility of claim 18 wherein the splice operation used to add an allosteric modulation in the modeled biochemical pathway.

24. The computer utility of claim 18 wherein the splice operation used to add a non-allosteric modulation in the modeled biochemical pathway.