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1. 发明申请

US20060241868A1 SYSTEM, METHOD, AND COMPUTER PRODUCT FOR SIMPLIFIED INSTRUMENT CONTROL AND FILE MANAGEMENT 审中-公开
标题翻译：用于简化仪器控制和文件管理的系统，方法和计算机产品
公开(公告)号：US20060241868A1
公开(公告)日：2006-10-26
申请号：US11279068
申请日：2006-04-07
申请人： Shaw Sun , Andrew Kimbrough , Luis Jevons , Gregory Fisher , Stephen Lincoln , Shantanu Kaushikkar
发明人： Shaw Sun , Andrew Kimbrough , Luis Jevons , Gregory Fisher , Stephen Lincoln , Shantanu Kaushikkar
IPC分类号： G06F19/00
CPC分类号： G16B50/00 , G16B25/00
摘要： 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.
摘要翻译：描述了用于管理从生物探针阵列生成的文件的系统的实施例，其包括产生包括多个原始强度值的第一数据文件的第一生成器，以及包含唯一地识别第一数据文件的第一标识符的元数据; 第二生成器，其产生包括多个经处理的强度值的第二数据文件，每个处理的强度值表示生物探针阵列上的探针特征;以及元数据，其包括不同于唯一地识别第二数据文件的第一标识符的第二标识符和指向第二数据文件的指针第一标识符以及文件索引器，其将第一和第二数据文件的元数据存储在高速缓存数据库中。

2. 发明申请

US20060167636A1 System, method, and computer software for the presentation and storage of analysis results 有权
公开(公告)号：US20060167636A1
公开(公告)日：2006-07-27
申请号：US11352008
申请日：2006-02-10
申请人： Shantanu Kaushikkar , Teresa Webster , Rui Mei , Linda McAllister
发明人： Shantanu Kaushikkar , Teresa Webster , Rui Mei , Linda McAllister
IPC分类号： G06F19/00
CPC分类号： G06F19/20 , B01J2219/007 , G01N2035/00158 , G06F19/18 , G06F19/26 , Y10S707/99943
摘要： A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data. The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.

3. 发明授权

US07031846B2 Method, system, and computer software for the presentation and storage of analysis results 有权
公开(公告)号：US07031846B2
公开(公告)日：2006-04-18
申请号：US10219882
申请日：2002-08-15
申请人： Shantanu Kaushikkar , Teresa Webster , Rui Mei , Linda McAllister
发明人： Shantanu Kaushikkar , Teresa Webster , Rui Mei , Linda McAllister
IPC分类号： G01N33/48 , C12Q1/68 , G06F7/00
CPC分类号： G06F19/20 , B01J2219/007 , G01N2035/00158 , G06F19/18 , G06F19/26 , Y10S707/99943
摘要： A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data, The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.

4. 发明申请

US20050033900A1 System, method, and computer software product for specifying parameters associated with a biological probe array 审中-公开
标题翻译：用于指定与生物探针阵列相关的参数的系统，方法和计算机软件产品
公开(公告)号：US20050033900A1
公开(公告)日：2005-02-10
申请号：US10930405
申请日：2004-08-31
申请人： Shantanu Kaushikkar
发明人： Shantanu Kaushikkar
IPC分类号： G01N33/53 , C12M1/00 , C12Q1/68 , C40B50/14 , G01N21/64 , G01N27/447 , G01N33/48 , G01N33/50 , G01N35/00 , G01N35/04 , G06F3/048 , G06F19/20 , G06F19/26 , G11C5/00
CPC分类号： G01N21/6452 , B01J2219/00527 , B01J2219/00533 , B01J2219/00585 , B01J2219/00596 , B01J2219/00605 , B01J2219/00612 , B01J2219/00659 , B01J2219/00675 , B01J2219/00677 , B01J2219/00689 , B01J2219/00695 , B01J2219/00702 , B01J2219/00707 , C40B50/14 , G01N27/44717 , G01N27/44721 , G01N2021/6419 , G01N2021/6421 , G01N2021/6441 , G01N2021/6471 , G01N2035/00158 , G01N2035/0494 , G16B25/00 , G16B45/00
摘要： Systems, methods, and computer program products are described for specifying a scanning area of a substrate. In accordance with one method, steps include receiving location data corresponding to a plurality of probe-feature locations on the substrate, storing the location data, accessing the location data, and scanning the substrate based on the accessed location data. A scanning system is described that includes a computer, a scanner, and a computer program product. The product, when executed on the computer, accesses location data corresponding to a plurality of probe-feature locations on a substrate, and controls the scanner's scanning of the substrate based on the accessed location data.
摘要翻译：描述了用于指定基板的扫描区域的系统，方法和计算机程序产品。根据一种方法，步骤包括接收对应于衬底上的多个探针特征位置的位置数据，存储位置数据，访问位置数据以及基于所访问的位置数据扫描衬底。描述了包括计算机，扫描仪和计算机程序产品的扫描系统。该产品在计算机上执行时访问与基板上的多个探针特征位置相对应的位置数据，并且基于所访问的位置数据来控制扫描仪对基板的扫描。

5. 发明申请

US20060217913A1 System, Method, and Computer Software Product for Gain Adjustment in Biological Microarray Scanner 审中-公开
标题翻译：系统，方法和计算机软件产品在生物微阵列扫描仪中的增益调整
公开(公告)号：US20060217913A1
公开(公告)日：2006-09-28
申请号：US11423605
申请日：2006-06-12
申请人： Shantanu Kaushikkar , Nathan Weiner , Eric McKenzie , John Stephens
发明人： Shantanu Kaushikkar , Nathan Weiner , Eric McKenzie , John Stephens
IPC分类号： G01R35/00
CPC分类号： G01N21/6452 , B01J2219/00527 , B01J2219/00533 , B01J2219/00585 , B01J2219/00596 , B01J2219/00605 , B01J2219/00612 , B01J2219/00659 , B01J2219/00675 , B01J2219/00677 , B01J2219/00689 , B01J2219/00695 , B01J2219/00702 , B01J2219/00707 , C40B50/14 , G01N27/44717 , G01N27/44721 , G01N2021/6419 , G01N2021/6421 , G01N2021/6441 , G01N2021/6471 , G01N2035/00158 , G01N2035/0494 , G16B25/00 , G16B45/00
摘要： In accordance with some embodiments of the present invention, a method for gain adjustment is described that comprises (a) receiving a user selection of one or more parameters that includes a first resolution value; (b) obtaining a plurality of pixel intensity values using the user selected parameters and a gain value, wherein the obtained pixel intensity values are representative of a distribution of pixel intensity values; (c) generating a measure of comparison between the representative distribution and a desired distribution of pixel intensity values; (d) adjusting the gain value using the measure of comparison; and (e) obtaining a plurality of pixel intensity values using a second resolution value and the adjusted gain value.
摘要翻译：根据本发明的一些实施例，描述了一种用于增益调整的方法，其包括：（a）接收包括第一分辨率值的一个或多个参数的用户选择; （b）使用用户选择的参数和增益值获得多个像素强度值，其中所获得的像素强度值表示像素强度值的分布; （c）产生代表性分布与像素强度值的期望分布之间的比较度量; （d）使用比较措施调整增益值; 和（e）使用第二分辨率值和调整后的增益值获得多个像素强度值。

6. 发明申请

US20110246085A1 System, method, and computer software for the presentation and storage of analysis results 有权
标题翻译：系统，方法和计算机软件，用于演示和存储分析结果
公开(公告)号：US20110246085A1
公开(公告)日：2011-10-06
申请号：US13161150
申请日：2011-06-15
申请人： Shantanu Kaushikkar , Teresa Webster , Rui Mei , Linda McAllister
发明人： Shantanu Kaushikkar , Teresa Webster , Rui Mei , Linda McAllister
IPC分类号： G06F19/00
CPC分类号： G06F19/20 , B01J2219/007 , G01N2035/00158 , G06F19/18 , G06F19/26 , Y10S707/99943
摘要： A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data. The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.
摘要翻译：描述了计算机程序产品以及相关系统和方法，其处理对应于生物探针阵列的探针的发射强度数据。所述计算机程序包括基因型和统计分析管理器，所述基因型和统计分析管理器至少部分地基于所述发射强度数据和至少一个用户可选择的统计参数的统计测量来确定绝对或相对表达值。至少部分地基于发射强度数据，分析管理器还可以确定对一个或多个探针的基因型呼叫。至少部分地基于至少一个用户可选显示参数和/或基因型呼叫之间的归一化变化的量度，分析管理器可进一步显示绝对或相对表达值。归一化变化的度量可以至少部分地基于基因型呼叫和参考值的比较。

7. 发明申请

US20060259874A1 System, method, and computer software product for linked window interfaces 有权
公开(公告)号：US20060259874A1
公开(公告)日：2006-11-16
申请号：US11389690
申请日：2006-03-27
申请人： Shantanu Kaushikkar , Luis Jevons
发明人： Shantanu Kaushikkar , Luis Jevons
IPC分类号： G06F17/00
CPC分类号： G01N21/6452 , B01J2219/00527 , B01J2219/00533 , B01J2219/00585 , B01J2219/00596 , B01J2219/00605 , B01J2219/00612 , B01J2219/00659 , B01J2219/00675 , B01J2219/00677 , B01J2219/00689 , B01J2219/00695 , B01J2219/00702 , B01J2219/00707 , C40B50/14 , G01N27/44717 , G01N27/44721 , G01N2021/6419 , G01N2021/6421 , G01N2021/6441 , G01N2021/6471 , G01N2035/00158 , G01N2035/0494 , G06F19/20 , G06F19/26
摘要： 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. When a user selects a feature from any of the two or more windows, a corresponding feature in at least one other of the two or more windows is highlighted.

8. 发明申请

US20050222777A1 System, method, and computer software prorduct for specifying parameters associated with a biological probe array 审中-公开
标题翻译：用于指定与生物探针阵列相关的参数的系统，方法和计算机软件
公开(公告)号：US20050222777A1
公开(公告)日：2005-10-06
申请号：US11133713
申请日：2005-05-20
申请人： Shantanu Kaushikkar
发明人： Shantanu Kaushikkar
IPC分类号： G01N33/53 , C12M1/00 , C12Q1/68 , C40B50/14 , G01N21/64 , G01N27/447 , G01N33/48 , G01N33/50 , G01N35/00 , G01N35/04 , G06F3/048 , G06F19/20 , G06F19/26 , G06F19/00
CPC分类号： G01N21/6452 , B01J2219/00527 , B01J2219/00533 , B01J2219/00585 , B01J2219/00596 , B01J2219/00605 , B01J2219/00612 , B01J2219/00659 , B01J2219/00675 , B01J2219/00677 , B01J2219/00689 , B01J2219/00695 , B01J2219/00702 , B01J2219/00707 , C40B50/14 , G01N27/44717 , G01N27/44721 , G01N2021/6419 , G01N2021/6421 , G01N2021/6441 , G01N2021/6471 , G01N2035/00158 , G01N2035/0494 , G16B25/00 , G16B45/00
摘要： Systems, methods, and computer program products are described for specifying a scanning area of a substrate. In accordance with one method, steps include receiving location data corresponding to a plurality of probe-feature locations on the substrate, storing the location data, accessing the location data, and scanning the substrate based on the accessed location data. A scanning system is described that includes a computer, a scanner, and a computer program product. The product, when executed on the computer, accesses location data corresponding to a plurality of probe-feature locations on a substrate, and controls the scanner's scanning of the substrate based on the accessed location data.
摘要翻译：描述了用于指定基板的扫描区域的系统，方法和计算机程序产品。根据一种方法，步骤包括接收对应于衬底上的多个探针特征位置的位置数据，存储位置数据，访问位置数据以及基于所访问的位置数据扫描衬底。描述了包括计算机，扫描仪和计算机程序产品的扫描系统。该产品在计算机上执行时访问与基板上的多个探针特征位置相对应的位置数据，并且基于所访问的位置数据来控制扫描仪对基板的扫描。

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