Abstract: Systems, methods, and computer program products are described for providing a graphical user interface (GUI) that may include a first openable window of image features constituting, for example, a pseudo-image of a scanned probe array. The image features each have one or more characteristics representing one or more hybridization reactions associated with a probe of the probe array. The GUI also has a second openable window including data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array. This second window may be, for example, a scatter plot of hybridization intensities of probes to two or more labeled samples. The GUI further includes a third openable window including descriptive features such as rows of a spreadsheet. Each row may include descriptive elements associated with a probe.

Abstract: Systems, methods, and computer program products are described for providing a graphical user interface (GUI) that may include a first openable window of image features constituting, for example, a pseudo-image of a scanned probe array. The image features each have one or more characteristics representing one or more hybridization reactions associated with a probe of the probe array. The GUI also has a second openable window including data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array. This second window may be, for example, a scatter plot of hybridization intensities of probes to two or more labeled samples. The GUI further includes a third openable window including descriptive features such as rows of a spreadsheet. Each row may include descriptive elements associated with a probe.

Abstract: An applications programming interface is described that includes code libraries that enable transfer of pixel data, intermediate results data, or both, from a data structure or data file directly or indirectly to a user-provided application. The pixel data and intermediate results data may include data from biological experiments related probe arrays.

Abstract: An embodiment of a method for consumable management is described that comprises acquiring a plurality of measures of sample quality, each sample associated with a well of a well plate; and providing a graphical representation of the well plate that includes a graphical representation of each of the wells and the associated measure of quality for the sample and to instruct users in the event of errors on how to recover. Additionally, an embodiment of the invention includes a method for handling pipette tip usage in a fluid handling system.

Abstract: Systems, methods, and computer program products are described for providing a graphical user interface (GUI) that may include a first openable window of image features constituting, for example, a pseudo-image of a scanned probe array. The image features each have one or more characteristics representing one or more hybridization reactions associated with a probe of the probe array. The GUI also has a second openable window including data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array. This second window may be, for example, a scatter plot of hybridization intensities of probes to two or more labeled samples. The GUI further includes a third openable window including descriptive features such as rows of a spreadsheet. Each row may include descriptive elements associated with a probe.

Abstract: An embodiment of a system for managing files generated from biological probe arrays is described that comprises a first generator that produces a first data file comprising a plurality of raw intensity values, and metadata comprising a first identifier that uniquely identifies the first data file; a second generator that produces a second data file comprising a plurality of processed intensity values each representing a probe feature on a biological probe array, and metadata comprising a second identifier different than the first identifier that uniquely identifies the second data file and a pointer to the first identifier; and a file indexer that stores the metadata for the first and second data files in a cache database.

Abstract: An applications programming interface is described that includes code libraries that enable transfer of pixel data, intermediate results data, or both, from a data structure or data file directly or indirectly to a user-provided application. The pixel data and intermediate results data may include data from biological experiments related probe arrays.

Abstract: An applications programming interface is described that includes code libraries that enable transfer of pixel data, intermediate results data, or both, from a data structure or data file directly or indirectly to a user-provided application. The pixel data and intermediate results data may include data from biological experiments related probe arrays.

Abstract: A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments are improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device.

Abstract: A data manager is described for providing a publish database for access by data mining tools and other data processing software applications. The data manager includes a results-for-publication identifier that identifies synthesized probe array results and spotted probe array results for publishing. This identification may be based, at least in part, on user selections. The data in the publish database is organized in accordance with an integrated database schema. The data manager may also include an experimental results registration processor that registers the synthesized probe array results and the spotted probe array results for publishing. This registration may be based, at least in part, on user selections. For example, a user may select certain probe array results from a graphical user interface displaying a tree of files containing probe array results from multiple experiments with synthesized and/or spotted probe arrays.

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: A data manager is described for providing a publish database for access by data mining tools and other data processing software applications. The data manager includes a results-for-publication identifier that identifies synthesized probe array results and spotted probe array results for publishing. This identification may be based, at least in part, on user selections. The data in the publish database is organized in accordance with an integrated database schema. The data manager may also include an experimental results registration processor that registers the synthesized probe array results and the spotted probe array results for publishing. This registration may be based, at least in part, on user selections. For example, a user may select certain probe array results from a graphical user interface displaying a tree of files containing probe array results from multiple experiments with synthesized and/or spotted probe arrays.

Abstract: An applications programming interface is described that includes code libraries that enable transfer of pixel data, intermediate results data, or both, from a data structure or data file directly or indirectly to a user-provided application. The pixel data and intermediate results data may include data from biological experiments related probe arrays.

Abstract: According to an embodiment of the present invention, a computer based method for managing information about a plurality of experiments conducted on a plurality of samples is provided. Each experiment provides an indication of a degree of expression of particular genetic sequences in a sample. The method includes a variety of steps such as registering at least one of the plurality of samples with a centralized database. The method then includes steps of tracking a plurality of information about the samples and tracking a plurality of information about the experiments. A step of producing a sample history about the plurality of samples from the plurality of information is also a part of the method. The method filters the information about the experiments and the information about the samples according to filters selected by a user. The information is made available for publishing to a variety of targets such as a public database.

Abstract: Systems, methods, and computer program products are described for providing a graphical user interface (GUI) that may include a first openable window of image features constituting, for example, a pseudo-image of a scanned probe array. The image features each have one or more characteristics representing one or more hybridization reactions associated with a probe of the probe array. The GUI also has a second openable window including data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array. This second window may be, for example, a scatter plot of hybridization intensities of probes to two or more labeled samples. The GUI further includes a third openable window including descriptive features such as rows of a spreadsheet. Each row may include descriptive elements associated with a probe.

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: A data manager is described for providing a publish database for access by data mining tools and other data processing software applications. The data manager includes a results-for-publication identifier that identifies synthesized probe array results and spotted probe array results for publishing. This identification may be based, at least in part, on user selections. The data in the publish database is organized in accordance with an integrated database schema. The data manager may also include an experimental results registration processor that registers the synthesized probe array results and the spotted probe array results for publishing. This registration may be based, at least in part, on user selections. For example, a user may select certain probe array results from a graphical user interface displaying a tree of files containing probe array results from multiple experiments with synthesized and/or spotted probe arrays.