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  Auto-analysis framework for sequence evaluationRelated Patent Categories: Data Processing: Measuring, Calibrating, Or Testing, Measurement System In A Specific Environment, Chemical Analysis, Specific Operation Control SystemThe Patent Description & Claims data below is from USPTO Patent Application 20070010953. Brief Patent Description - Full Patent Description - Patent Application Claims
CLAIM OF PRIORITY [0001] This application is a continuation of U.S. patent application Ser. No. 10/650,470 filed Aug. 28, 2003, which claims priority to U.S. Provisional Patent Application No. 60/407,439, entitled "Auto-Analysis Framework for Sequence Evaluation", filed Aug. 28, 2002, all of which are hereby incorporated by reference. BACKGROUND [0002] 1. Field [0003] The present teachings relate to biological laboratory instruments and, more particularly to a system and methods for integrating large numbers of instruments and analysis applications into an automated framework. [0004] 2. Description of the Related Art [0005] Biological analysis is often a complex process that involves many different instruments and associated analysis applications. In genomic and molecular biological studies, large numbers of samples may be processed by sequencers, fluorometers, mass spectrometers, and other instruments to provide data, indicative of the composition or expression of nucleotide or protein components comprising the sample. Captured data is subsequently provided to one of a number of different applications for further processing and analysis. The analysis applications are typically software-based and may perform such tasks as sequence determination, mutational analysis, single nucleotide polymorphism (SNP) identification, etc. In certain implementations, a number of applications may be required to process the data from a variety of different samples in order to complete the analysis. These applications may be configured to operate serially wherein the resultant data output by one application is used as input for another application. When operating in this mode, the data must be properly organized and configured in the manner which is expected by each application. Typically, such operations are performed by an investigator and means to better automate the process are lacking in the industry. Likewise, parallel data processing to achieve improved throughput often requires investigator coordination, monitoring, and review thus limiting the potential to more fully automate the analysis process. [0006] As biological laboratories become increasingly complex with more associated instruments and analysis applications, the difficulty of integrating the analysis applications and instruments into a unified system amenable to automated analysis becomes more complex. Hence, there is a need for systems and methods which permit improved integration of instruments and analysis applications in biological laboratory environment. SUMMARY [0007] The aforementioned needs are satisfied by the present teachings which, in one aspect, comprise a system for integrating a plurality of biological data acquisition instruments that obtain electronic data from physical data samples with a plurality of data analysis applications. The system comprises a plurality of instrument components associated with the instruments that capture identification information and data from the biological samples and at least one registry component defining a suitable instrument protocol for each of the plurality of instrument components and an application protocol for each of the data analysis applications. In various embodiments, the system further comprises an application manager component that communicates with the plurality of instrument components and the plurality of data analysis applications and further has access to the information contained in the at least one registry component. The application manager utilizes the information contained in the at least one registry component to determine appropriate data and information to be sent and received from the biological instruments, as well as, determining the type and format of data to be provided to the analysis applications. In one aspect, the applications manager component further recognizes an analysis protocol to be used to perform a desired data analysis procedure. The applications manager sends/receives data, information and instructions to/from analysis applications so as to provide a means to conduct multi-step analysis which require interaction between a plurality of software applications and/or instruments. [0008] The applications manager may further provide a user interface whereby an investigator can program or schedule biological analysis routines for one or more samples by selecting instruments identified in the registry to capture the data from the biological sample and selecting the one or more analysis applications from the registry to receive and process the electronic data. In various embodiments, additional instruments and analysis applications can be incorporated into the system by registering the instrument component protocols and analysis application protocols in the registry as desired or as they become available. [0009] In another aspect, the present teachings provide a system for integrating a plurality of biological data instruments that acquire electronic data from physical biological samples with a plurality of discrete data analysis applications that receive the electronic data from the biological data instruments. The system may be configured to operate in such a manner so as to provide a degree of transparency between the instruments and applications such that the data formatting, transmission, and storage is handled without special or custom configuration of either the instruments or applications. This feature improves scalability of the system and allows for a more flexible means to maintain/upgrade components of the system. [0010] The system further comprises a plurality of instrument components respectively associated with the biological data instruments and the at least one registry containing instrument protocols for each of the plurality of instruments and protocols for each of the data analysis applications, wherein the data analysis protocol includes a messaging protocol. In this aspect, the system further comprises an application manager that communicates with the plurality of instrument components and the plurality of data analysis applications via a standardized communications protocol wherein the application manager has access to the at least one registry and includes an associated user interface such that the user can program a series of biological analysis operations to be performed via the user interface such that selected biological samples may be processed by desired instruments. Upon completion of the processing of the biological samples, the data may be made available to selected data analysis applications for subsequent processing. In this aspect, the application manager automatically makes the data available to the data analysis application(s) via an appropriate communications protocol by notifying the data analysis application(s) of the location and/or address of the data or by distributing the information directly to the application itself. [0011] In yet another aspect, the present teachings describe a system for integrating a plurality of biological data instruments that obtain data from samples, with a plurality of data analysis applications, wherein the system comprises a plurality of instrument components respectively associated with the instruments that capture identification information from the samples, at least one registry containing instrument protocols for each of the plurality of instrument components and protocols for each of analysis applications wherein the protocols for the analysis applications includes a format protocol indicative of the format required by a selected analysis application to process data from one of the plurality of instruments. The system in this aspect further comprises a management component that communicates with a plurality of instrument components and the plurality of analysis applications and has access to the at least one registry. In this particular implementation, the manager component includes a user interface that provides a means for a user to select one or more instruments to be used to conduct a biological analysis. The user interface further provides means for selecting particular samples to be analyzed and can further direct the resultant data obtained from particular instruments to be provided to appropriate analysis applications. In this aspect, the applications manager provides instructions to the instrument component associated with selected instruments such that the instrument component will output the data in a desired format as indicated by the format protocol in the registry and specified for the selected analysis application that is to receive the data from the instrument component. [0012] From the foregoing, it will be appreciated that the system and methods of the present teachings permit a scalable environment in which to conduct biological analysis and further provide greater flexibility in terms of adding or changing instruments and analysis applications. Furthermore, integration of the application manager into the system improves data transparency throughout the analysis environment and facilitates design and implementation of automated routines. These and other objects and advantages of the present teachings will become more apparent from the following description taken in conjunction with the accompanying drawings. BRIEF DESCRIPTION OF THE DRAWINGS [0013] FIG. 1 is a block diagram of a biological analysis system with a management and registry component that permit enhanced automation of the system; [0014] FIG. 2 is an exemplary flow chart illustrating how new instruments and analysis applications can be added into the system of FIG. 1; [0015] FIG. 3 is a block diagram which illustrates one exemplary organization of a registry service that is a component of the system of FIG. 1; [0016] FIG. 4A is a block diagram graphically illustrating the components used by an investigator to program a biological sample evaluation or run; [0017] FIG. 4B is an exemplary flow chart illustrating one manner in which the investigator can program the system of FIG. 1 to conduct biological analysis for a plurality of samples; [0018] FIG. 4C illustrates exemplary screen shots of the information that can be provided to the investigator programming the system of FIG. 1; [0019] FIG. 5 is a diagram illustrating the operation of the system of FIG. 1 during a biological analysis run; [0020] FIG. 6A is an exemplary screen shot illustrating status information that can be provided by the system of FIG. 1 during a biological analysis run; and Continue reading... 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