Abstract: A data mining tool is described that includes a data structure populator that stores one or more first sets of data selected for querying into a first data structure. The tool also has a query builder that builds at least a first query based, at least in part, on one or more query parameters. Also included in the tool is a query manager that interrogates the first data structure with the first query. The one or more first sets of data are based, at least in part, on experiments using both synthesized probe arrays and spotted probe arrays.

Abstract: Systems and methods are described that may be applied to scanning biological materials in or on probe arrays. For example, a system is described that includes a scanner that has one or more excitation sources and an emission receiving element, such as an objective lens, that receives from locations of the probe array an emission signal responsive to the excitation sources. The scanner also has a radial position generator that generates radial positions of the emission receiving element. Also included in the system is a computer memory having stored therein a plurality of position data, each representing a radial position of the emission receiving element. Also stored in the computer memory unit is a set of comparator instructions that generate a clock signal based, at least in part, on comparing one or more of the plurality of radial positions with one or more of the plurality of position data.

Abstract: An attachment device is described for attaching a part to a structure. The part may be, for example, an optical element such as a lens or a mirror, that is to be attached, for example, to an optical instrument such as a scanner used to scan biological materials. The device includes a base and two or more holding elements coupled to the base. The holding elements may include a first group of two or more opposing holding elements of a first length and a second group of two or more opposing holding elements of a second length shorter than the first length. Each holding element flexibly engages at least one surface of the part when the device is engaged with the part. A third group of two or more opposing holding elements may also be provided that also are shorter than the first length and that rigidly engage the part. The base and the holding elements may be formed of a single piece of flexible material.

Abstract: An apparatus is described that includes an emission signal detector and an emission signal filter. An excitation beam scans an array of biological materials, and the emission signal detector detects an emission signal indicative of an emission beam responsive to the excitation beam. The emission signal filter is a linear-phase filter that provides a filtered emission signal having substantially symmetrical rise and fall edges. A linear-phase excitation signal filter may also be provided that provides a filtered excitation signal having substantially symmetrical rise and fall edges. The emission signal filter and the excitation signal filter may be matched. In some applications, they may be high-order Bessel filters. Linear-phase filtering enables sampling of emission signals to be accomplished consistently irrespective of the scanning direction, and thus is particularly advantageous in bi-directional scanning applications.

Abstract: Labeled targets on a support synthesized with polymer sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, can be detected by exposing marked regions of sample to radiation from a source and detecting the emission therefrom, and repeating the steps of exposition and detection until the sample is completely examined.