Abstract: Methods are disclosed for predicting the performance of oligonucleotide probes by identifying the sequence of a candidate probe, generating experimental data for the probe and using the data to train a statistical regression model. Nucleic acid arrays containing probes with performance predicted by the described using methods are provided. Also included are algorithms for performing the subject methods recorded on computer-readable media, and computational systems for analysis.

Abstract: Comparative genomic hybridization is a tool that compares DNA samples from suspect cells of an organism with DNA samples from normal cells. Cross-species comparative genomic hybridization visualization allows genomic data from model organisms to be mapped and presented in accordance with the (for example) human genome to suggest possible common biological effects between two or more species.

Abstract: Probe selection methods, computer program products, systems and arrays are provided. The probes can be used, for example, in genome scanning applications such as array CGH and/or location analysis.

Abstract: There are a number of sensors (2, 22) such as thermocouples which can provide a putative measurand signal which is within a predicted range for such signals whilst the sensor is incorrectly operating, such as as due to an open circuit. Techniques and processes are available to determine by interrogation sensor operational validity, but these can distort the measurand signal if correct. By time division multiplex techniques the present arrangement takes a putative measurand signal from a sensor (2, 22) in order that either within the same time division or more normally a separate time division, an interrogation of the sensor is performed in order to determine accuracy and therefore validity of the sensor 22.

Abstract: A method of ensuring the integrity of read-only components in deployed mixed-mode applications that includes generating a digital fingerprint prior to the deployment of a mixed-mode application is discussed. The digital fingerprint is based on a read-only component in the mixed-mode application and uniquely identifies the read-only component. The method also deploys the mixed-mode application and the digital fingerprint. Additionally, the method verifies, at execution time by using the digital fingerprint, that the read-only component in the mixed-mode deployed application that served as the basis for the digital fingerprint is identical to the same read-only component originally packaged with the mixed-mode application.

Abstract: The present invention is directed toward automatically integrating a late bound program language into an external environment. The external environment may be an early bound environment, a late bound environment or some combination thereof. Associated with the late bound program environment is a modular execution engine and an interface mechanism, wherein the interface mechanism is capable of expressing late bound semantics in a format compatible with the external environment.

Abstract: Systems, methods and computer readable media for extracting data from features on a chemical array, using a feature extraction module including feature extraction algorithms configured to calculate characteristics of array features. A reference table is provided that associates probe names of probes contained on the array with at least one additional identifier. The reference table is accessible by the feature extraction module to convert any one of the at least one additional identifiers to the probe names, and the probe names to at least one of the at least one additional identifiers.

Abstract: Methods, systems and computer readable media for downloading data to file depository managed on a server. A user locates a remote server that hosts a file to be downloaded to the file depository using a web browser. A download request is submitted to the download queue, wherein the download queue is executed to download the file into the file depository. The system checks remote FTP sites and updates its file depository at specific intervals set by users and downloads the latest version of its file and archives old versions. The system allows users to upload files from the file depository to remote servers and updates the file depository if the file transfer was successful. All file transfer history for downloads/uploads may be viewable by client users.

Abstract: The present invention relates to certain benzotriazole carboxylic acid or ester derivatives of Formula (I), pharmaceutically acceptable salts and solvates thereof, which exhibit useful pharmaceutical properties, for example, as agonists for the GPCR referred to as hRUP38. Also provided by the present invention are pharmaceutical compositions containing compounds of the invention, and methods of using the compounds and compositions of the invention in the prophylaxis or treatment of metabolic-related disorders, including dyslipidemia, atherosclerosis, coronary heart disease, insulin resistance, type 2 diabetes, Syndrome-X and the like.

Abstract: There is provided a two-stage optical regenerator for regenerating a data signal comprising a series of optical pulses. Each stage of the optical regenerator comprises a modulator for modulating a reference signal with an input signal, and an interferometer for causing the modulated reference signal to interfere with another version of the modulated reference signal delayed by less than one bit period of the data signal to regenerate the input signal. The input signal of the modulator of the first stage of the regenerator comprises the data signal, and the input signal of the modulator of the second stage of the regenerator comprises the output from the first stage of the regenerator.

Abstract: Systems and methods for using the same to obtain one or more probe sequences, e.g., for use on an array, are provided. Also provided are computer program products for executing the subject methods.

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.

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.

Abstract: Apparatus and methods are disclosed for printing a plurality of biopolymer features on the surfaces of substrates. An apparatus comprises a substrate mount for receiving a substrate, a dispensing device for dispensing reagents for synthesizing a biopolymer on a surface of the substrate, an optical system for positioning the substrate mount along a y-axis and an optical system for positioning the dispensing device along an x-axis. The apparatus may comprise a touch system for positioning the substrate and the dispensing device along a z-axis. One of the substrate mount or the dispensing device is adapted for translation along the y-axis and for rotation about a central axis that is parallel to a z-axis. The other of the above is adapted to move along the x-axis transversely to the direction of, and independently of, movement of the one adapted for translation along the y-axis. The optical systems cooperate to position the substrate mount and the dispensing device relative to one another.

Abstract: A method and system for cropping a digital image of multiple individual microarrays. Various embodiments of the present invention include, a digital image of multiple individual microarrays projected along a first coordinate axis by summing columns of pixel intensity values. A transformation maps the projected pixel intensity values to a transform in a frequency domain. A filter function is constructed from a power spectrum of the transform and multiplied by the transform to obtain a filtered transform. The filtered transform is mapped back to the spatial domain to give the filtered, spatial-domain image. The filtered, spatial-domain image is used to determine the coordinates of boundaries separating the individual microarrays along the first coordinate axis. The multi-pack of microarrays is rotated, and the method may be repeated for a second coordinate axis that is perpendicular to the first coordinate axis. The boundaries are used to identify the boundaries separating individual microarrays.

Abstract: Methods and systems for identifying and selecting nucleic acid probes for detecting a target with a nucleic acid probe array or microarray, comprising selecting a plurality of candidate probes, forming a plurality of clusters from the plurality of candidate probes according to hybridization characteristics of the candidate probes, forming at least one SuperCluster from the clusters; and selecting at least one probe from each SuperCluster for the probe array.

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, 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: Methods and compositions for encoding and decoding array information on an array are provided. The methods involve contacting an array containing one or more array information features with a sample containing target that binds to at least one of the one or more array information features to produce at least one signal that provides information about the array.