Graphic design of combinatorial material libraries

• US 20070185657A1
• Filed: 04/02/2007
• Published: 08/09/2007
• Est. Priority Date: 10/19/1998
• Status: Abandoned Application

• Current Assignee: Freeslate Inc. (Unchained Labs Inc.)
• Original Assignee: Symyx Technologies Incorporated (Dassault Systemes SA)
• Inventors: Wang, Pei, McFarland, Eric, Safir, Adam, Turner, Stephen, Lacy, Steven, Erden, Lynn
• Application Number:
  US11/732,408
• Publication Number:
  US 20070185657A1
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry
• CPC Class Codes: G16C 20/62 Design of libraries

Abstract

Computer-implemented methods, programs and apparatus for generating a library design for a combinatorial library of materials. A library design includes a set of sources representing components to be used in preparing the combinatorial library, destinations representing arrangements of cells and mappings, defining one or more distribution patterns for assigning components to cells in the destination arrangement or arrangements. Mappings include gradients and sets of user-defined equations, and are used to calculate the amount of one or more components to be assigned to a cell or cells in an arrangement. A library design can also include one or more process parameters defined to vary over time or across a plurality of destination cells. The invention outputs a data file defining the library design, including electronic data representing the sources, the destinations and the mapping, in a format suitable for implementing manually or using automated material handling apparatus.

Claims

1. A computer-implemented method for generating a library design for a library of materials, comprising:

providing a graphical user interface including a workspace for designing a library of materials;

defining one or more sources and one or more destinations, each source being electronic data representing a chemical or mixture of chemicals to be used in preparing the library of materials and each destination being electronic data representing an arrangement of cells;

displaying a visual representation of one or more of the one or more defined destinations in the workspace of the graphical user interface, each destination representation including a representation of one or more cells in the corresponding arrangement;

receiving first user input defining a first mapping, the first mapping being electronic data defining a gradient distribution pattern for assigning a first chemical or mixture of chemicals represented by one of the one or more defined sources to a plurality of cells in the one or more defined destinations, the input specifying a minimum and a maximum amount of the first chemical or mixture of chemicals to be assigned to any of the plurality of cells and a gradient to be applied between the minimum and maximum amounts of the first chemical or mixture of chemicals across the plurality of cells;

receiving second user input defining a second mapping, the second mapping being electronic data defining a second distribution pattern describing an amount or amounts of a second chemical or mixture of chemicals to be distributed to one or more selected cells in the one or more arrangements, the one or more selected cells including one or more of the plurality of cells;

using the first mapping and the second mapping to determine amounts of the first chemical or mixture of chemicals and the second chemical or mixture of chemicals to be deposited in each of the one or more selected cells included in the plurality of cells; and

modifying the visual representation of the one or more defined destinations to include a visual indication of the determined amounts of the first and second chemicals or mixtures of chemicals.

2. The method of claim 1, further comprising:

generating a set of synthesis instructions for use by one or more synthesis instruments to create the library of materials based on the defined sources, destinations, and mappings.

3. The method of claim 1, wherein the first input defining a first mapping comprises a selection from a set of available mapping types, the set of available mapping types comprising a one to one mapping of a chemical or mixture of chemicals from a source to a cell in the one or more arrangements and a one to many mapping of a chemical or mixture of chemicals from a source to a plurality of cells in the one or more arrangements.

4. The method of claim 3, wherein the set of available mapping types further comprises a many to many mapping of a plurality of chemicals or mixtures of chemicals from a plurality of sources to a plurality of cells in the one or more arrangements.

5. The method of claim 4, wherein the set of available mapping types further comprises a many to one mapping of a plurality of chemicals or mixtures of chemicals from a plurality of sources to a cell in the one or more arrangements.

6. The method of claim 1, wherein the second distribution pattern includes electronic data identifying a fixed amount of the second chemical or mixture of chemicals to be distributed to one or more cells in the one or more arrangements.

7. The method of claim 1, wherein the second input specifies a second gradient distribution pattern according to a minimum and a maximum amount of the second chemical or mixture of chemicals to be assigned to a second plurality of cells of the one or more arrangements and a second gradient to be applied between the minimum and maximum amounts of the second chemical or mixture of chemicals across the second plurality of cells.

8. The method of claim 1, further comprising:

receiving user input modifying one or more of the first and second mappings; and

modifying the visual representation of the one or more defined destinations according to the one or more modified mappings.

9. The method of claim 1, further comprising:

receiving third user input defining one or more parameters, each parameter being electronic data corresponding to a process parameter to be applied to one or more cells in the one or more the arrangements and defining a parameter value for the one or more cells in the one or more arrangements, the third user input defining a scheme for varying the parameter values for at least one of the parameters across two or more cells in the one or more arrangements; and

modifying the visual representation of the one or more defined destinations to include a visual indication of the parameter values.

10. The method of claim 9, wherein:

the parameter value for one or more of the parameters is defined to vary over time for one or more cells in the one or more arrangements.

11. A computer program product on a computer-readable medium for generating a library design for a library of materials, the computer program product comprising instructions operable to cause a programmable processor to:

provide a graphical user interface including a workspace for designing a library of materials;

receive an input defining one or more sources and one or more destinations, each source being electronic data representing a chemical or mixture of chemicals to be used in preparing the library of materials and each destination being electronic data representing an arrangement of cells;

display a visual representation of one or more of the one or more defined destinations in the workspace of the graphical user interface, each destination representation including a representation of one or more cells in the corresponding arrangement;

receive first user input defining a first mapping, the first mapping being electronic data defining a gradient distribution pattern for assigning a first chemical or mixture of chemicals represented by one of the defined sources to a plurality of cells in the one or more defined destinations, the input specifying a minimum and a maximum amount of the first chemical or mixture of chemicals to be assigned to any of the plurality of cells and a gradient to be applied between the minimum and maximum amounts of the first chemical or mixture of chemicals across the plurality of cells;

receive second user input defining a second mapping, the second mapping being electronic data defining a second distribution pattern describing an amount or amounts of a second chemical or mixture of chemicals to be distributed to one or more selected cells in the one or more arrangements, the one or more selected cells including one or more of the plurality of cells;

use the first mapping to determine amounts of the first chemical or mixture of chemicals to be deposited in each of the plurality of cells and the second mapping to determine the amount or amounts of the second chemical or mixture of chemicals to be deposited in each of the one or more selected cells, wherein the amounts of the first and second chemicals or mixture of chemicals to be deposited in each of the one or more selected cells that are included in the plurality of cells are determined according to both the first mapping and the second mapping; and

modify the visual representation of the one or more defined destinations to include a visual indication of the determined amounts of the first and second chemicals or mixtures of chemicals.

12. The computer program product of claim 11, further comprising instructions operable to cause a programmable processor to:

generate a set of synthesis instructions for use by one or more synthesis instruments to create the library of materials based on the defined sources, destinations, and mappings.

13. The computer program product of claim 11, wherein the first input defining a first mapping comprises a selection from a set of available mapping types, the set of available mapping types comprising a one to one mapping of a chemical or mixture of chemicals from a source to a cell in the one or more arrangements and a one to many mapping of a chemical or mixture of chemicals from a source to a plurality of cells in the one or more arrangements.

14. The computer program product of claim 13, wherein the set of available mapping types further comprises a many to many mapping of a plurality of chemicals or mixtures of chemicals from a plurality of sources to a plurality of cells in the one or more arrangements.

15. The computer program product of claim 14, wherein the set of available mapping types further comprises a many to one mapping of a plurality of chemicals or mixtures of chemicals from a plurality of sources to a cell in the one or more arrangements.

16. The computer program product of claim 11, wherein the second distribution pattern includes electronic data identifying a fixed amount of the second chemical or mixture of chemicals to be distributed to one or more cells in the one or more arrangements.

17. The computer program product of claim 11, wherein the second input specifies a second gradient distribution pattern according to a minimum and a maximum amount of the second chemical or mixture of chemicals to be assigned to a second plurality of cells of the one or more arrangements and a second gradient to be applied between the minimum and maximum amounts of the second chemical or mixture of chemicals across the second plurality of cells.

18. The computer program product of claim 11, further comprising instructions operable to cause a programmable processor to:

receive an input modifying one or more of the first and second mappings; and

modify the visual representation of the one or more defined destinations according to the one or more modified mappings.

19. The computer program product of claim 11, further comprising instructions operable to cause a programmable processor to:

receive third user input defining one or more parameters, each parameter being electronic data corresponding to a process parameter to be applied to one or more cells in the one or more the arrangements and defining a parameter value for the one or more cells in the one or more arrangements, the third user input defining a scheme for varying the parameter values for at least one of the parameters across two or more cells in the one or more arrangements; and

modify the visual representation of the one or more defined destinations to include a visual indication of the parameter values.

20. The computer program product of claim 19, wherein:

the parameter value for one or more of the parameters is defined to vary over time for one or more cells in the one or more arrangements.

21. A computer-implemented method for generating a library design for a library of materials, comprising:

defining a set of one or more sources and one or more destinations, each source being electronic data representing a chemical or mixture of chemicals to be used in preparing the library of materials and each destination being electronic data representing an arrangement of cells;

receiving an input defining a mapping scheme for assigning the chemicals or mixtures of chemicals represented by the one or more sources to cells in the one or more destinations, the input specifying a set of equations for calculating amounts of the chemicals or mixtures of chemicals to be assigned to the cells in the one or more destinations;

using the set of equations to calculate a composition of a plurality of materials to be prepared in the cells in the one or more destinations; and

displaying a visual representation of the one or more defined destinations, the visual representation including a visual indication of the calculated compositions.

22. The method of claim 21, wherein at least one of the set of equations is selected from the group consisting of:

a ratio equation defining an amount of one of the chemicals or mixtures of chemicals to be assigned to one or more of the cells as a function of an amount of another chemical or mixture of chemicals to be assigned to the one or more of the cells;

a volume equation defining an amount of one of the chemicals or mixtures of chemicals to be assigned to one or more of the cells as a function of a total volume of a plurality of chemicals or mixtures of chemicals to be assigned to the one or more of the cells; and

a mass equation defining an amount of one of the chemicals or mixtures of chemicals to be assigned to one or more of the cells as a function of a total mass of a plurality of chemicals or mixtures of chemicals to be assigned to the one or more of the cells.

23. The method of claim 21, wherein using the set of equations comprises solving the set of equations using matrix algebra techniques.

24. The method of claim 21, wherein:

the input defining the mapping scheme comprises input associating the sources and equations with cells or groups of cells in the defined destinations; and

using the equations comprises calculating the composition of a material to be prepared in a given cell based on the equations and sources associated with the given cell.

25. The method of claim 21, further comprising:

in response to the input defining the mapping scheme, displaying a visual indication of the equations associated with the cells or groups of cells in the defined destinations.

26. The method of claim 21, wherein:

defining the one or more sources comprises associating one or more of the chemicals or mixtures of chemicals with a type representing a class of chemicals to be used in preparing the library of materials;

receiving user input specifying a mapping scheme comprises receiving input specifying one or more of the set of equations as a function of the type; and

using the equations comprises solving the equations specified as a function of the type for a given destination cell or group of cells by substituting the corresponding chemical or chemicals associated with the type.

27. A computer program product on a computer-readable medium for generating a library design for a combinatorial library of materials, the computer program product comprising instructions operable to cause a programmable processor to:

define a set of one or more sources and one or more destinations, each source being electronic data representing a chemical or mixture of chemicals to be used in preparing the library of materials and each destination being electronic data representing an arrangement of cells;

receive an input defining a mapping scheme for assigning the chemicals or mixtures of chemicals represented by the one or more sources to cells in the one or more destinations, the input specifying a set of equations for calculating amounts of the chemicals or mixtures of chemicals to be assigned to the cells in the one or more destinations;

use the set of equations to calculate a composition of a plurality of materials to be prepared in the cells in the one or more destinations; and

display a visual representation of the one or more defined destinations, the visual representation including a visual indication of the calculated compositions.

28. The computer program product of claim 27, wherein at least one of the plurality of equations is selected from the group consisting of:

a ratio equation defining an amount of one of the chemicals or mixtures of chemicals to be assigned to one or more of the cells as a function of an amount of another chemical or mixture of chemicals to be assigned to the one or more of the cells;

a volume equation defining an amount of one of the chemicals or mixtures of chemicals to be assigned to one or more of the cells as a function of a total volume of a plurality of chemicals or mixtures of chemicals to be assigned to the one or more of the cells; and

a mass equation defining an amount of one of the chemicals or mixtures of chemicals to be assigned to one or more of the cells as a function of a total mass of a plurality of chemicals or mixtures of chemicals to be assigned to the one or more of the cells.

29. The computer program product of claim 27, wherein the instructions operable to cause a programmable processor to use the set of equations comprise instructions to solve the set of equations using matrix algebra techniques.

30. The computer program product of claim 27, wherein:

the input defining the mapping scheme comprises input associating the sources and equations with cells or groups of cells in the defined destinations; and

the instructions operable to cause the programmable processor to use the equations comprise instructions operable to cause the programmable processor to calculate the composition of a material to be prepared in a given cell based on the equations and sources associated with the given cell.

31. The computer program product of claim 27, further comprising instructions operable to cause the programmable processor to:

in response to the input defining the mapping scheme, display a visual indication of the equations associated with the cells or groups of cells in the defined destinations.

32. The computer program product of claim 27, wherein:

the instructions operable to cause the programmable processor to define the one or more sources comprise instructions operable to cause the programmable processor to associate one or more of the chemicals or mixtures of chemicals with a type representing a class of chemicals to be used in preparing the library of materials;

the instructions operable to cause the programmable processor to receive user input specifying a mapping scheme comprise instructions operable to cause the programmable processor to receive input specifying one or more of the set of equations as a function of the type; and

the instructions operable to cause the programmable processor to use the equations comprise instructions operable to cause the programmable processor to solve the equations specified as a function of the type for a given destination cell or group of cells by substituting the corresponding chemical or chemicals associated with the type.