System, method, and computer software prorduct for specifying parameters associated with a biological probe array

Abstract

Systems, methods, and computer program products are described for specifying a scanning area of a substrate. In accordance with one method, steps include receiving location data corresponding to a plurality of probe-feature locations on the substrate, storing the location data, accessing the location data, and scanning the substrate based on the accessed location data. A scanning system is described that includes a computer, a scanner, and a computer program product. The product, when executed on the computer, accesses location data corresponding to a plurality of probe-feature locations on a substrate, and controls the scanner's scanning of the substrate based on the accessed location data.

1 . A method comprising the steps of: 
 (a) receiving location data corresponding to a plurality of probe-feature locations on a substrate;    (b) storing the location data;    (c) accessing the location data; and    (d) scanning the substrate based, at least in part, on the accessed location data.    
   
   
       2 - 36 . (canceled)  
   
   
       37 . A method of programming a biopolymer array scanner to scan a plurality of biopolymeric arrays, said method comprising: individually selecting a scanning parameter for at least two different biopolymeric arrays of said plurality prior to using said scanner to scan said plurality of arrays.  
   
   
       38 . The method according to  claim 37 , wherein said scanning parameter is a scan region.  
   
   
       39 . The method according to  claim 37 , wherein said scanning parameter is a detector sensitivity setting for a first channel.  
   
   
       40 . The method according to  claim 39 , wherein said scanning parameter is a photo-multiplier tube setting for said first channel.  
   
   
       41 . The method according to  claim 37 , wherein said scanning parameter is a detector sensitivity setting for a second channel.  
   
   
       42 . The method according to  claim 41 , wherein said scanning parameter is a photo-multiplier tube setting for said second channel.  
   
   
       43 . The method according to  claim 37 , wherein said scanning parameter is a dye channel.  
   
   
       44 . The method according to  claim 37 , wherein said scanning parameter is an output file path.  
   
   
       45 . The method according to  claim 37 , wherein said scanning parameter is a barcode on the surface of the array substrate.  
   
   
       46 . The method according to  claim 37 , wherein said scanning parameters are set through retrieval of said parameters from a database via scanning of barcodes on the surface of said at least two different biopolymeric arrays.  
   
   
       47 . The method according to  claim 37 , wherein said at least one of said individually selected scanning parameters is a default parameter.  
   
   
       48 . The method according to  claim 37 , wherein the biopolymeric array is an array of polynucleotides or polypeptides.  
   
   
       49 . A computer-readable medium comprising program that allows an array scanner to be programmed according to the method of  claim 37 .  
   
   
       50 . The computer readable medium according to  claim 49 , wherein said program provides a user interface which presents to a user the option of individually selecting at least one scanning parameter for two or more of a plurality of slides.  
   
   
       51 . A biopolymer array scanner comprising a computer-readable medium according to  claim 49 .  
   
   
       52 . A biopolymer array scanner according that allows a user to program it according to the method of  claim 1 .  
   
   
       53 . A method of scanning a plurality of biopolymeric arrays, said method comprising: (a) programming a biopolymer array scanner according to the method of  claim 37;  and (b) scanning said plurality of biopolymeric arrays arrays using said programmed scanner.  
   
   
       54 . The method of  claim 53 , wherein the biopolymeric array is an array of polynucleotides or polypeptides.  
   
   
       55 . The method of  claim 53 , further comprising transmitting said result from a first location to a second location.  
   
   
       56 . The method of  claim 55 , where said second location is a remote location.  
   
   
       57 . A method comprising receiving data representing said result of a scan obtained by the method of  claim 56 .  
   
   
       58 . A kit for use in a biopolymer array optical scanner, said kit comprising: (a) a computer-readable medium according to  claim 49;  and (b) instructions for operating said scanner according to said programming.