SYSTEMS AND METHODS FOR PRODUCING CHEMICAL ARRAY LAYOUTS

• US 20100267588A1
• Filed: 06/29/2010
• Published: 10/21/2010
• Est. Priority Date: 12/15/2005
• Status: Active Grant

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Shukla, Amitabh, Gao, Jing, Nelson, Charles F.
• Granted Patent: US 9,286,438 B2
• Time in Patent Office: Days
• US Class Current: 506/24
• 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

Abstract

Systems and methods for using the same to obtain a chemical array layout are provided. Also provided are computer program products for executing the subject methods.

Claims

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

(A) an input manager for receiving array request information from a user;

(B) a processing module comprising;

(i) an array set developer configured to;

(a) identify a total number of features required to array display a selected portion of probe content of array request information; and

(b) evaluate whether said identified total number of features exceeds a single array format feature number limit to determine whether a single array format or an array set of two or more array formats is required to array display said total number of features to provide an array set decision; and

(ii) 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 an array set layout for an array set of two or more array formats based on application of one or more of plurality of rules to information that includes array request information received from a user and said array set decision; and

(C) an output manager for providing a first version of said array set layout to said user.

2. The system of claim 1, wherein said selected portion is the entire probe content of said array request information.

3. The system of claim 1, wherein said selected portion is less than the entire probe content of said array request information.

4. The system of claim 1, wherein said array set developer communicates said array set decision to said user for acceptance prior to providing said array set decision to said array layout developer.

12. The system according to claim 1, wherein a memory further stores a plurality of versions of said array set layout.

13. The system of claim 12, wherein at least two of the versions are generated in response to input from a single user.

14. The system of claim 13, wherein at least two of the versions are generated in response to input from at least two users.

15. The system of claim 13, wherein the processing module further comprises a differencing engine for comparing the at least two versions.

16. The system of claim 15, wherein the output manager communicates with an interface which displays differences between compared versions.

17. The system of claim 16, wherein a second version may be modified by a user to include a characteristic of the first version.

18. The system of claim 17, wherein a new version of the array layout is generated which incorporates the modification.

21. The system of claim 1, wherein said rules are modifiable by a permitted user of said system.

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

23. The system of claim 1, wherein the array format 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.

24. The system of claim 23, wherein the system-defined parameters include user-defined layout parameters.

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

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

(ii) an array request information manager to provide a history of said array request information to a user;

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

(iv) an array layout customizing manager configured to receive a customer input array layout and suggest an alternative layout developed from information not provide by a user;

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

(vi) a default probe set selection manager that allows a user to include or exclude a predetermined set of probes in said array layout.

34. A method of producing an array layout for a chemical array, said method comprising:

receiving into a system according to claim 1, an array request information from a user; and

obtaining an array layout from said system to produce said array layout.

35. The method according to claim 34, wherein said receiving is via the Internet.

36. The method according to claim 35, wherein said receiving is via a graphical user interface.

5-11. -11. (canceled)

19-20. -20. (canceled)

26-33. -33. (canceled)

37-38. -38. (canceled)

39. 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, operates said computer to:

(a) receive chemical array request information from a user;

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

(c) provide said array set layout to a user.