Population pharmacokinetic modeling and analysis (PDX-POP™)

• US 20060161408A1
• Filed: 03/15/2006
• Published: 07/20/2006
• Est. Priority Date: 10/19/2001
• Status: Abandoned Application

• Current Assignee: David Young, Marc R. Gastonguay, Sian F. Bigora, William J. Bachman
• Original Assignee: David Young, Marc R. Gastonguay, Sian F. Bigora, William J. Bachman
• Inventors: Gastonguay, Marc R., Bigora, Sian F., Bachman, William J., Young, David
• Application Number:
  US11/375,753
• Publication Number:
  US 20060161408A1
• Time in Patent Office: Days
• US Class Current: 703/11
• 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
• CPC Class Codes: G16C 20/30 Prediction of properties of chemical compounds, compositions or mixtures

Abstract

A biological modeling system and method for enhanced computer-aided analysis of biological response data provides information synthesized from multiple sources. An executable model of a biological system is developed from information and structures based on multiple sources. In a preferred embodiment, biological data sets are selected by a user from a first active viewer window on a user computer display. A model is created and then run using integrated pharmacokinetic software. The output is next analyzed using integrated analysis tools. Once analyzed, the model is balanced to ensure that it matches the information and structures. Once the model is created, run, and balanced, it can be used to draw attention to important relations through integrated reporting functions. This program could be run with such programs as NONMEM®.

Claims

1. In combination, a computer executable pharmacokinetic model of a biological system, a computer executable data editor, a computer executable report generator, a data stream representing a chemical level within said biological system at a particular time period, a computer system including nonvolatile storage, a memory and a processor, and a computer executable integrator, said computer executable integrator having:

a locator that searches for at least one component of said computer executable pharmacokinetic model of a biological system, and searches for at least one model building aid for population analysis, said computer executable data editor, and said computer executable report generator through a search within said nonvolatile storage,

said at least one model building aid for population analysis facilitating data set checkout by having visualization of at least one observed variable and covariates and plots to reveal errors in a data file, exploration and visualization having plots, stepwise generalized additive modeling (GAM) and tree based modeling, and model diagnostics having residual plots and plots to check the validity of assumptions specific to non-linear mixed effects models, candidate covariate identification and model comparison;

a protocol for a control stream selected based upon said locator search which will execute said computer executable pharmacokinetic model of a biological system;

a modeler that generates said control stream responsive to said protocol for a control stream;

a data function that initiates execution of said computer executable data editor,

and manages execution of said computer executable report generator responsive to said locator search; and

a means to save a configuration responsive to a result from at least one of said locator search, said protocol said modeler, and said data function.

2. The combination of a computer executable pharmacokinetic model of a biological system, a computer executable data editor, a computer executable report generator, a data stream representing a chemical level within said biological system at a particular time period, a computer system including nonvolatile storage a memory and a processor, and a computer executable integrator of claim 1, wherein said computer executable integrator further comprises a conversion protocol operative to translate said data stream between a data format used by said computer executable pharmacokinetic model of a biological system and a data format used by said computer executable data editor, said conversion protocol responsive to said locator search.

3. The combination of a computer executable pharmacokinetic model of a biological system, a computer executable data editor, a computer executable report generator, a data stream representing a chemical level within said biological system at a particular time period, a computer system including nonvolatile storage, a memory and a processor, and a computer executable integrator of claim 1, wherein said computer executable integrator further comprises a conversion protocol operative to translate said data stream between a data format used by said computer executable pharmacokinetic model of a biological system and a data format used by said computer executable report generator, said conversion protocol responsive to said locator search.

5. The combination of a computer executable pharmacokinetic model of a biological system, a computer executable data editor, a computer executable report generator, a data stream representing a chemical level within said biological system at a particular time period, a computer system including nonvolatile storage, a memory and a processor, and a computer executable integrator of claim 1, wherein said data function is responsive to said locator search.

7. The combination of a computer executable pharmacokinetic model of a biological system, a computer executable data editor, a computer executable report generator, a data stream representing a chemical level within said biological system at a particular time period, a computer system including nonvolatile storage, a memory and a processor, and a computer executable integrator of claim 1, wherein said modeler generates a plurality of control streams for executing a plurality of data streams representing chemical levels within said biological system.

8. The combination of a computer executable pharmacokinetic model of a biological system, a computer executable data editor, a computer executable report generator, a data stream representing a chemical level within said biological system at a particular time period, a computer system including nonvolatile storage, a memory and a processor, and a computer executable integrator of claim 1, further comprising a means to choose a computer programming language compiler.

9. The combination of a computer executable pharmacokinetic model of a biological system, a computer executable data editor, a computer executable report generator, a data stream representing a chemical level within said biological system at a particular time period, a computer system including nonvolatile storage, a memory and a processor, and a computer executable integrator of claim 1, wherein said computer executable pharmacokinetic model of a biological system further comprises a third-party computer executable pharmacokinetic model of a biological system operable separately and independently from said combination.

10. The combination of a computer executable pharmacokinetic model of a biological system, a computer executable data editor, a computer executable report generator, a data stream representing a chemical level within said biological system at a particular time period, a computer system including nonvolatile storage, a memory and a processor, and a computer executable integrator of claim 1, wherein said computer executable report generator further comprises a third-party computer executable report generator operable separately and independently from said combination.

22. The combination of a computer executable pharmacokinetic model of a biological system, a computer executable data editor, a computer executable report generator, a data stream representing a chemical level within said biological system at a particular time period, a computer system including nonvolatile storage, a memory and a processor, and a computer executable integrator of claim 1, further comprising a means for displaying in real time the run-time output from said computer executable pharmacokinetic model of a biological system.

4. (canceled)

6. (canceled)

11. In combination, a computer executable pharmacokinetic model of a biological system operable separately and independently from said combination, a computer executable data editor, a computer executable report generator operable separately and independently from said combination, a data stream representing a chemical level within said biological system at a particular time period, a computer system including data storage and a processor, and a computer executable integrator, said computer executable integrator comprising:

a locator that searches from within said data storage and locates at least one component of said computer executable pharmacokinetic model of a biological system;

a protocol for a control stream which will execute said computer executable pharmacokinetic model of a biological system responsive to said locator search;

a modeler that generates said control stream responsive to said control stream protocol;

said locator further distinguishing said computer executable data editor;

a means to control execution of said computer executable data editor responsive to said locator distinguishing;

a conversion protocol operative to translate said data stream between a data format used by said computer executable pharmacokinetic model of a biological system and a data format used by said computer executable data editor, said conversion protocol responsive to said locator search;

said locator further identifying said computer executable report generator;

a data function that is compatible with and manages execution of said computer executable report generator responsive to said locator identifying; and

a conversion protocol operative to translate said data stream between a data format used by said computer executable pharmacokinetic model of a biological system and a data format used by said computer executable report generator, said conversion protocol responsive to said locator search.

21. The combination computer executable pharmacokinetic model of a biological system, computer executable data editor, computer executable report generator, data stream representing a chemical level within said biological system at a particular time period, computer system including data storage and a processor, and computer executable integrator of claim 11, further comprising a means to save a configuration responsive to a result from at least one of said locating means, said protocol establishing means, said control stream generating means, said computer executable data editor distinguishing means, and said computer executable report generator identification means.

12. In combination, a computer executable pharmacokinetic model of a biological system, a computer executable data editor, a computer executable report generator, a data stream representing a chemical level within said biological system at a particular time period, and a computer system having a display window, a memory and a processor, wherein the improvement comprises a computer executable control center having:

a user interface displayed within said display window;

a computer executable integrator having a protocol for converting an output from ones of said computer executable pharmacokinetic model of a biological system said computer executable data editor, and said computer executable report generator to an input of ones of said computer executable pharmacokinetic model of a biological system, said computer executable data editor, and said computer executable report generator;

said computer executable report generator having at least one model building aid for population analysis facilitating data set checkout by having visualization of at least one observed variable and covariates and plots to reveal errors in a data file, exploration and visualization having plots and modeling, and model diagnostics having residual plots and plots to check the validity of assumptions specific to non-linear mixed effects models, candidate covariate identification and model comparison;

a user control panel displayed within said user interface which is operative in combination with user input to launch each of said computer executable pharmacokinetic model of a biological system, said computer executable data editor, and said computer executable report generator; and

a display of output from said computer executable pharmacokinetic model of a biological system in said user interface.

13. The combination of a computer executable pharmacokinetic model of a biological system, a computer executable data editor, a computer executable report generator, a data stream representing a chemical level within said biological system at a particular time period, and a computer system having a display window, a memory and a processor of claim 12, further comprising a means to choose between compiling said data stream and executing a full modeling operation of said computer executable pharmacokinetic model of a biological system using said data stream.

14-20. -20. (canceled)