Patents by Inventor Derek Bernhart
Derek Bernhart has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 7451047Abstract: 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.Type: GrantFiled: August 31, 2005Date of Patent: November 11, 2008Assignee: Affymetrix, Inc.Inventors: Luis Jevons, Derek Bernhart, Nga Yu Cheung, Conrad Sheppy
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Publication number: 20060074563Abstract: 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.Type: ApplicationFiled: August 31, 2005Publication date: April 6, 2006Applicant: Affymetrix, INC.Inventors: Luis Jevons, Derek Bernhart, Nga Cheung, Conrad Sheppy
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Patent number: 6954699Abstract: 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.Type: GrantFiled: February 19, 2003Date of Patent: October 11, 2005Assignee: Affymetrix, Inc.Inventors: Luis Jevons, Derek Bernhart, Nga Yu Cheung, Conrad Sheppy
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Publication number: 20050186581Abstract: 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.Type: ApplicationFiled: March 1, 2004Publication date: August 25, 2005Applicant: AFFYMETRIX, INC.Inventors: Mark Chee, Chunwei Wang, Luis Jevons, Derek Bernhart, Robert Lipshutz
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Publication number: 20050108197Abstract: 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.Type: ApplicationFiled: October 12, 2004Publication date: May 19, 2005Applicant: Affymetrix, INC.Inventors: Luis Jevons, Derek Bernhart, Conrad Sheppy
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Patent number: 6804679Abstract: 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.Type: GrantFiled: March 8, 2002Date of Patent: October 12, 2004Assignee: Affymetrix, Inc.Inventors: Luis Jevons, Derek Bernhart, Conrad G. Sheppy
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Publication number: 20030220748Abstract: Computer-aided techniques for analyzing biological sequences like nucleic acids are provided. The computer system may analyze hybridization intensities indicating hybridization affinity between nucleic acid probes and a sample nucleic acid sequence in order to call bases in the sample sequence. Multiple base calls may be combined to form a single base call. Additionally, the computer system may analyze hybridization intensities in order to monitor gene expression or the change in gene expression as compared to a baseline.Type: ApplicationFiled: May 15, 2003Publication date: November 27, 2003Applicant: AFFYMETRIX, INC., a California corporationInventors: Teresa A. Webster, MacDonald S. Morris, Michael P. Mittmann, David J. Lockhart, Ming-Hsiu Ho, Derek Bernhart, Luis C. Jevons
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Publication number: 20030157545Abstract: 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.Type: ApplicationFiled: February 19, 2003Publication date: August 21, 2003Applicant: Affymetrix, INC.Inventors: Luis Jevons, Derek Bernhart, Nga Yu Cheung, Conrad Sheppy
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Patent number: 6600996Abstract: Computer-aided techniques for analyzing biological sequences like nucleic acids are provided. The computer system may analyze hybridization intensities indicating hybridization affinity between nucleic acid probes and a sample nucleic acid sequence in order to call bases in the sample sequence. Multiple base calls may be combined to form a single base call. Additionally, the computer system may analyze hybridization intensities in order to monitor gene expression or the change in gene expression as compared to a baseline.Type: GrantFiled: March 28, 1997Date of Patent: July 29, 2003Assignee: Affymetrix, Inc.Inventors: Teresa A. Webster, MacDonald S. Morris, Michael P. Mittmann, David J. Lockhart, Ming-Hsiu Ho, Derek Bernhart, Luis C. Jevons
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Publication number: 20020183933Abstract: Computer-aided techniques for analyzing biological sequences like nucleic acids are provided. The computer system may analyze hybridization intensities indicating hybridization affinity between nucleic acid probes and a sample nucleic acid sequence in order to call bases in the sample sequence. Multiple base calls may be combined to form a single base call. Additionally, the computer system may analyze hybridization intensities in order to monitor gene expression or the change in gene expression as compared to a baseline.Type: ApplicationFiled: March 28, 1997Publication date: December 5, 2002Inventors: TERESA A. WEBSTER, MACDONALD S. MORRIS, MICHAEL P. MITTMANN, DAVID J. LOCKHART, DEREK BERNHART, LUIS C. JEVONS
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Publication number: 20020147512Abstract: Systems, methods, and computer program products are described that provide an applications programming interface (API) for enabling a user-provided software application to access a data structure of a laboratory information management system application. The API includes one or more code libraries that enable transfer of user data from the user-provided software application directly or indirectly to the data structure. The user data includes data from a number of biological experiments. The transfer may be a batch transfer of data from more than one experiment. The biological experiments may be based on the use of synthesized arrays and/or spotted arrays. The code libraries may also enable exporting of data directly or indirectly from the data structure to the user-provided software application, which may include a data-mining tool, an image-processing tool, and/or a data-processing tool.Type: ApplicationFiled: March 1, 2002Publication date: October 10, 2002Applicant: Affymetrix, Inc.Inventors: Derek Bernhart, Daniel M. Bartell, Wehib Zewde, Rajindar S. Nijor
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Publication number: 20020128993Abstract: 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.Type: ApplicationFiled: March 8, 2002Publication date: September 12, 2002Applicant: Affymetrix, Inc.Inventors: Luis Jevons, Derek Bernhart, Conrad G. Sheppy
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Publication number: 20020059326Abstract: Systems, methods, and computer program products are described, including a method having the steps of providing one or more identifiers, specifying one or more attributes for at least one of the identifiers, generating a data template including the identifier, and receiving by the data template a first value for the identifier in accordance with the one or more attributes. The value is related to use of a probe array. The method may also include storing the first value in a data structure, which may be included in a database. The data template may be an experiment data template or a sample data template. Other steps may include storing image data of a probe array in the data structure; analyzing the image data to generate results data; storing the results data in the data structure; and/or tracking the first value, the image data, and the result data.Type: ApplicationFiled: July 19, 2001Publication date: May 16, 2002Inventors: Derek Bernhart, Rajindar S. Nijor