Systems and methods for producing chemical array layouts

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.

1 . A 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 the 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 layout for a single array format or an array set of two or more array formats based on the application of one or more of the 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 an array layout to a 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 developer communicates said array set decision to said user for acceptance prior to providing said array set decision to said array layout developer.  
   
   
       5 . The system of  claim 1 , wherein when said array set decision is that a single array format can array display said total number of array features, said array layout developer develops an array layout for a single array format.  
   
   
       6 . The system of  claim 1 , wherein when said array set decision is that an array set of two or more array formats is required to array display said total number of array features, said array layout developer develops an array set layout.  
   
   
       7 . The system according to  claim 6 , wherein at least a portion of the probe content of said total number of features is distributed among the features of said array set layout in a random fashion.  
   
   
       8 . The system according to  claim 6 , wherein at least a portion of the probe content of said total number of features is distributed among the features of said array set layout in a non-random fashion.  
   
   
       9 . The system of  claim 6 , wherein said array set layout includes at least one probe group of features that is present in each array format of said array set.  
   
   
       10 . The system according to  claim 9 , wherein said at least one probe group is a control probe group.  
   
   
       11 . The system according to  claim 9 , wherein said at least one probe group is an experimental probe group.  
   
   
       12 . The system according to  claim 1 , wherein a memory further stores a plurality of versions of an array 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.  
   
   
       19 . The system of  claim 16 , wherein a second version may be modified by a user to eliminate a characteristic of the second version not present in the first version.  
   
   
       20 . The system of  claim 19 , wherein a new version of the array layout is generated which incorporates the modification.  
   
   
       21 . The system of  claim 1 , wherein the rules are modifiable by a permitted user of the system.  
   
   
       22 . The system of  claim 1 , wherein the array layout comprises the 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, 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.    
   
   
       26 . The system according to claim 1 , wherein said system comprises a communication module that provides for remote communication between a user and said processor module.  
   
   
       27 . The system according to  claim 26 , wherein said communication module provides for communication between said user and said chemical processor module via the Internet.  
   
   
       28 . The system according to  claim 27 , wherein said communication module provides for a graphical user interface (GUI) between said user and said processing module.  
   
   
       29 . A method of obtaining an array layout for a chemical array, said method comprising: 
 inputting array request information into a system according to  claim 1;  and    obtaining an array layout from said system.    
   
   
       30 . The method according to  claim 29 , wherein said inputting is via the Internet.  
   
   
       31 . The method according to  claim 29 , wherein said inputting is via a graphical user interface.  
   
   
       32 . The method according to  claim 29 , wherein said method further comprises ordering one or more chemical arrays having said array layout via said system from a chemical array vendor.  
   
   
       33 . The method according to  claim 32 , wherein said method further comprises receiving said one or more ordered chemical arrays from said chemical array vendor.  
   
   
       34 . A method of producing an array layout for a chemical array, said method comprising: 
 receiving from a user array request information into a system according to  claim 1;  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.  
   
   
       37 . The method according to  claim 34 , wherein said method further comprises producing one or more chemical arrays having said array layout.  
   
   
       38 . The method according to  claim 37 , wherein said method further comprises shipping said one or more chemical arrays to a customer.  
   
   
       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 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 layout to a user.