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.

Abstract: Methods, systems and computer readable media for controlling an instrument in communication with a host computer are provided. Operations of an instrument that must be completed on schedule are controlled via an embedded controller embedded in the instrument. A complete status packet is sent to a host computer from the embedded controller. Periodically, the embedded controller repeats the sending of a complete status packet to the host computer, wherein status values in the complete status packet are updated with each iteration of sending a complete status packet.

Abstract: A method of selecting a set of normalization probes for use on a comparative genome hybridization array is provided. In certain embodiments, the method includes: a) selecting a first region of a genome to be evaluated by comparative genome hybridization to produce data; b) selecting a second region of the genome for normalization of the data, and c) selecting from a set of candidate probes a sub-set of normalization probes that detect the second region.

Abstract: A slide cover for enclosing a region comprising an active region on a slide is provided. A slide cover and a slide are also provided. A slide cover for enclosing a region comprising an active region on a slide, where the slide is placed in a clamshell slide holder is also provided.

Abstract: A slide cover for enclosing a region comprising an active region on a slide is provided. A slide cover and a slide are also provided. A slide cover for enclosing a region comprising an active region on a slide, where the slide is placed in a clamshell slide holder is also provided.

Abstract: Methods, systems and computer readable media for controlling an instrument in communication with a host computer are provided. Operations of an instrument that must be completed on schedule are controlled via an embedded controller embedded in the instrument. A complete status packet is sent to a host computer from the embedded controller Periodically, the embedded controller repeats the sending of a complete status packet to the host computer, wherein status values in the complete status packet are updated with each iteration of sending a complete status packet.

Abstract: A method of selecting a set of normalization probes for use on a comparative genome hybridization array is provided. In certain embodiments, the method includes: a) selecting a first region of a genome to be evaluated by comparative genome hybridization to produce data; b) selecting a second region of the genome for normalization of the data, and c) selecting from a set of candidate probes a sub-set of normalization probes that detect the second region.

Abstract: Aspects of the invention include methods of systems of pairwise filtering candidate probe nucleic acid sequences. Aspects of the invention further include methods and systems of selecting candidate probe nucleic acid sequences from plurality thereof, which methods and systems employ a pairwise elimination ranked record of a plurality of candidate probe nucleic acids for a genomic region of interest.

Abstract: Systems and methods for using the same to select one or more comparative genome hybridization (CGH) probes specific for a sub-genomic region of interest are provided. Also provided are computer program products for executing the subject methods.

Abstract: Methods and reagents are disclosed which provide for more sensitive, more accurate and higher through-put analyses of target nucleic acid sequences. The methods and reagents of the present invention may be generically applied to generally any target nucleic acid sequence and do not require a priori information about the presence, location or identity of mutations in the target nucleic acid sequence. The reagents of the invention are mixtures of oligonucleotide precursors having a high level of coverage and mass number complexity, and also having tags analyzable by mass spectrometry which are covalently linked to the precursors through cleavable bonds. A method is also disclosed for analyzing a target nucleic acid sequence employing the mixtures of oligonucleotide precursors having tags analyzable by mass spectrometry covalently linked to the oligonucleotide precursors through cleavable bonds, and chemical or enzymatic assays to alter the mass of the oligonucleotide precursors prior to mass spectral analysis.

Abstract: A method in which an array identifier for a chemical array with probes at multiple feature locations is retrieved from a memory or read. The array identifier, a request for a test which requires an instruction on reading or processing the signal data read from the array, and payment information, are all forwarded to a remote location. A method is also provided which includes retrieving an instruction on reading or processing signal data read from a chemical array. This is retrieved from a memory using a test request and which memory carries one or more instructions for the array each retrievable with a different test request. Apparatus and computer program products are further provided.

Abstract: A method and apparatus for fabricating an array of biopolymers on a substrate using a biopolymer or biomonomer fluid, and using a dispensing head. The head has a reservoir chamber and at least one jet which can dispense droplets onto a substrate. The jet includes a capillary delivery chamber communicating with the reservoir chamber, which delivery chamber has an orifice. The jet further includes an ejector which, when activated, causes a droplet to be ejected from the orifice. The method includes loading the head by positioning the head with the orifice adjacent and facing a biomonomer or biopolymer fluid, and providing a load pressure to the reservoir chamber. The load pressure is sufficiently negative such that the fluid is drawn into the reservoir chamber through the orifice and delivery chamber, while simultaneously being insufficient to result in ambient atmosphere entering the delivery chamber through the orifice once the head has been loaded and no further fluid is facing and adjacent the orifice.

Abstract: A method of fabricating an addressable array of biopolymer probes on a substrate according to a target array pattern using a deposition apparatus, and a deposition apparatus which can execute the method and computer program products for the apparatus. The deposition apparatus which, when operated according to a target drive pattern based on nominal operating parameters of the apparatus, provides the probes on the substrate in the target array pattern. The method includes examining at least one operating parameter for an error from a nominal value which error will result in use of the target drive pattern producing a discrepancy between the target array pattern and an actual array pattern deposited. When an error is detected deriving, based on the error, a corrected drive pattern different from the target drive pattern such that use of the corrected drive pattern results in a reduced discrepancy between the target and actual array patterns.

Abstract: A method, apparatus, and computer program, for fabricating multiple arrays arranged successively in a first direction on a substrate and each having multiple feature sets arranged successively in the first direction within the array. The method uses a head system having multiple successive sets of dispensers. In the method, the head system is advanced in the first direction over the substrate while dispensing drop sets for each array from dispenser sets so as to form the arrays. In one aspect, drop sets are dispensed in an order the reverse of that from which the dispenser sets pass over a given location on the substrate as the head system advances in the first direction. In this case, each dispenser set deposits a drop set at a distance ahead of a drop set deposited by a preceding dispenser set which is less than the distance to the successive drop dispenser set which deposits the next drop set.

Abstract: A method, apparatus, and computer program products for fabricating multiple chemical arrays on a substrate, each array having multiple rows of feature locations with arrays of different sets being arranged in a sideways orientation with respect to the rows. The method includes dispensing drops from a drop dispensing head onto the substrate while maintaining a gap between the head and substrate and moving them relative to one another along a path so as to fabricate the arrays. The path for the relative moving includes moving the head in a direction along the rows of a first array set then moving the head in an opposite direction along the rows of a second array set. This pattern is repeated with the second array set of an earlier cycle being the first array set of a later cycle.

Abstract: Methods of identifying a sequence of a nucleic acid that is suitable for use as a surface immobilized probe for two or more mRNA transcripts encoded by the same gene are provided. In practicing the subject methods, a consensus region for the two or more transcripts is first identified, and this identified consensus region is then employed to identify the suitable nucleic acid sequence, e.g., by using a probe design protocol. The subject invention also includes algorithms for performing the subject methods recorded on a computer readable medium, as well as computational analysis systems that include the same. Also provided are nucleic acid arrays produced with probes having sequences identified by the subject methods, as well as methods for using the same.

Abstract: A drop deposition apparatus, and a method and computer program products using the drop deposition apparatus, for fabricating at least one addressable array of biopolymers on a substrate. The drop deposition apparatus has a drop dispenser unit and a sensing element. The method comprises includes for each of multiple addresses, dispensing droplets carrying the biopolymers or biopolymer precursors from a drop dispenser unit onto the sensing element, and onto the substrate so as to fabricate the array. Electrical signals resulting from dispensed droplets striking the sensing element are detected. A performance characteristic of the deposition apparatus is evaluated based on the detected signals.

Abstract: Methods, apparatus, and computer program, for use in fabricating a chemical array. The method may use an apparatus which includes a head system, a transport system, and a processor. The head system has multiple groups of drop dispensers which move in unison, each group having multiple dispensers. The transport system can move the head system with respect to a substrate with different dispensers of the groups following respective paths. The processor can dispense droplets from dispensers during operation of the transport system, in a pattern along a selected path for each group so as to form the array. The method includes identifying an error in one or more dispensers. When a dispenser of a first group is in error, then a second dispenser of each group is moved along the selected path for its group while dispensing droplets from at least the second dispenser of the first group in at least part of the pattern for the selected path of the first group.

Abstract: A method and apparatus for fabricating an array of biopolymers on a substrate using a biopolymer or biomonomer fluid, and using a dispensing head. The head has a reservoir chamber and at least one jet which can dispense droplets onto a substrate. The jet includes a capillary delivery chamber communicating with the reservoir chamber, which delivery chamber has an orifice. The jet further includes an ejector which, when activated, causes a droplet to be ejected from the orifice. The method includes loading the head by positioning the head with the orifice adjacent and facing a biomonomer or biopolymer fluid, and providing a load pressure to the reservoir chamber. The load pressure is sufficiently negative such that the fluid is drawn into the reservoir chamber through the orifice and delivery chamber, while simultaneously being insufficient to result in ambient atmosphere entering the delivery chamber through the orifice once the head has been loaded and no further fluid is facing and adjacent the orifice.

Abstract: A method, apparatus and computer program product, for fabricating an array of biopolymers on a substrate. The method uses a biopolymer or biomonomer fluid and a drop dispenser having a chamber into which the fluid is loaded and an orifice communicating with the chamber from which the fluid is dispensed. The method includes, when the chamber is loaded, applying a prime pressure to the fluid which varies over a range sufficient to move fluid within the drop dispenser but insufficient to cause fluid to be dispensed from the orifice. Drops are dispensed from the dispenser to the substrate so as to form the array.