Systems for producing chemical array layouts

• US 8,380,441 B2
• Filed: 11/30/2004
• Issued: 02/19/2013
• Est. Priority Date: 11/30/2004
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Webb, Peter G., Nelson, Charles F., Shukla, Amitabh, Munson, Marylinn
• Primary Examiner(s): NEGIN, RUSSELL SCOTT
• Application Number:
  US11/001,700
• Publication Number:
  US 20060116825A1
• Time in Patent Office: 3,003 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: B01J 2219/007 Simulation or vitual synthesis
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/30 Microarray design
• CPC Class Codes: G16H 10/40 for data related to laboratory analysis, e.g. patient specimen analysis

Abstract

Systems to obtain a chemical array layout are provided. Systems of the invention include input and output managers for receiving information from and sending information to one or more users and a processing module having an array layout developer that applies rules relating to array layout design. The array layout developer develops an array layout based on the application of one or more of the rules to array request information received from one or more users. Also provided are computer program products for executing the subject methods.

Claims

1. A system for producing an array layout, said system comprising:

(a) an input manager for receiving array request information from one or more users;

(b) a processing module comprising;

(i) an array layout developer having a memory comprising a plurality of rules relating to array layout design, wherein said array layout developer is configured to develop one or more array layout versions based on the application of one or more of the rules to information that includes the array request information received from the one or more users;

(ii) an array customizing manager configured to allow said array layout developer to develop an array layout that includes a first set of probe sequences provided by a first user and a second set of probe sequences provided by an additional party, wherein said second set of probe sequences is approved by the first user; and

(iii) a differencing engine for comparing a first of said one or more array layout versions to one or more second array layouts; and

(c) an output manager for providing said first array layout version and differences between said first array layout version and said one or more second array layouts to the one or more users in a user-readable format.

2. The system of claim 1, wherein the array layout developer develops a plurality of array layout versions that are stored in the memory.

3. The system of claim 2, wherein at least two of the plurality of array layout versions are generated in response to input from a single user.

4. The system of claim 2, wherein at least two of the plurality of array layout versions are generated in response to input from at least two users.

5. The system of claim 1, wherein said one or more second array layouts is a second array layout version of said one or more array layout versions developed by said array layout developer.

6. The system of claim 5, wherein said second array layout version may be modified by the one or more users to include a characteristic of the first array layout version.

7. The system of claim 6, wherein a new version of the array layout is generated which incorporates the modification.

8. The system of claim 5, wherein said second array layout version may be modified by the one or more users to eliminate a characteristic of the second array layout version not present in the first version.

9. The system of claim 8, wherein a new version of the array layout is generated which incorporates the modification.

10. The system of claim 1, wherein the rules are modifiable by a permitted user of the system.

11. The system of claim 1, wherein rules are modified in response to input provided to the system relating to probe performance on an array.

12. The system of claim 1, wherein rules are modified in response to input provided to the system relating to performance of an array having a particular layout.

13. The system of claim 1, wherein the layout comprises the organization of probe content on the array.

14. The system of claim 1, wherein the layout comprises system-defined layout parameters selected from the group consisting of numbers of features, density of features, dimensions of features, shape of features, size of interfeature areas, size of inter-array areas, and organization of probe content.

15. The system of claim 14, wherein the organization of probe content includes placement of features comprising selected probe sequences on an array.

16. The system of claim 14 wherein the system-defined parameters include user-defined layout parameters.

17. The system of claim 1, further comprising one or more of the following:

(i) an array request information manager to provide a history of said array request information to the one or more users;

(ii) an array layout format manager configured to provide an array layout format based on said array request information;

(iii) an array layout customizing manager configured to receive an array layout input by the one or more users and suggest an alternative layout developed from information not provided by the one or more users;

(iv) an array layout comparison manager configured to compare the one or more array layout versions to a database of one or more array layouts; and

(v) a default probe set selection manager that allows the one or more users to include or exclude a predetermined set of probes in said one or more array layout versions.

18. The system according to claim 17, wherein said system comprises an array request information manager to provide a history of said array request information to a user.

19. The system according to claim 17, wherein said system comprises an array layout format manager configured to provide an array layout format based on said chemical array request information.

20. The system according to claim 19, wherein said array layout format is optimized according to at least one predetermined parameter.

21. The system according to claim 20, wherein said at least one predetermined parameter is cost.

22. The system according to claim 17, wherein said system comprises an array layout customizing manager configured to receive a customer input array layout and suggest an alternative layout developed from information not provide by said user.

23. The system according to claim 17, wherein said system comprises an array layout comparison manager configured to compare an array layout to a database of one or more array layouts.

24. The system according to claim 23, wherein said array layout comparison manager is configured to provide a choice of an alternative array layout from said database to a user if a predetermined parameter is satisfied.

25. The system according to claim 1, wherein said additional party is a vendor of chemical arrays.

26. The system according to claim 1, wherein said system comprises a communication module that provides for remote communication between the one or more users and said processing module.

27. The system according to claim 26, wherein said communication module provides for communication between said one or more users and said processing module via the Internet.

28. The system according to claim 26, wherein said communication module provides for a graphical user interface (GUI) between said one or more users and said processing module.

29. The system of claim 1, wherein the array customizing manager is further configured to evaluate the first set of probe sequences and suggest an additional set of probe sequences.

30. A computer program product comprising a computer readable storage medium having a computer program stored thereon, wherein said computer program, when loaded onto a computer, controls said computer to:

(a) receive chemical array request information from one or more users;

(b) develop an array layout based on said received information by applying one or more array layout design rules to said received information;

(c) include in the array layout a first set of probe sequences provided by a first user and a second set of probe sequences provided by an additional party, wherein said second set of probe sequences is approved by the first user;

(d) compare said array layout to one or more second array layouts; and

(e) provide said array layout and differences between said array layout and said one or more second array layouts to the one or more users in a user-readable format.

31. The computer program product according to claim 30, wherein said computer program further controls said computer to perform at least one of the following additional tasks:

(i) provide a history of said array request information to the one or more users;

(ii) provide the array layout format to the one or more users based on said array request information;

(iii) receive an array layout input by the one or more users and suggest an alternative layout developed from information not provided by the one or more users; and

(iv) allow the one or more users to include or exclude a predetermined set of probes in the array layout.