System and method for discovery of biological instruments

• US 6,909,974 B2
• Filed: 06/04/2003
• Issued: 06/21/2005
• Est. Priority Date: 06/04/2002
• Status: Active Grant

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Dodgen, Stephen L., Fang, Sylvia H., Yung, Kai, Rohrlich, John
• Primary Examiner(s): Raymond, Edward
• Application Number:
  US10/455,264
• Publication Number:
  US 20040034478A1
• Time in Patent Office: 748 Days
• Field of Search: 702/31, 702/19, 702/20, 702/23, 702/30, 702/32, 340/539.12, 340/3.1
• US Class Current: 702/31
• CPC Class Codes: G05B 15/02 electric
• CPC Class Codes: G05B 23/0264 Control of logging system, e.g. decision on which data to store; time-stamping measurements
• CPC Class Codes: G05B 23/0267 Fault communication, e.g. human machine interface [HMI]
• CPC Class Codes: G06Q 50/00 Information and communication technology [ICT] specially adapted for implementation of business processes of specific business sectors, e.g. utilities or tourism healthcare informatics G16H
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/20 Heterogeneous data integration
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures
• CPC Class Codes: G16H 10/40 for data related to laboratory analysis, e.g. patient specimen analysis
• CPC Class Codes: G16H 40/20 for the management or administration of healthcare resources or facilities, e.g. managing hospital staff or surgery rooms
• CPC Class Codes: G16H 40/40 for the management of medical equipment or devices, e.g. scheduling maintenance or upgrades
• CPC Class Codes: G16H 40/63 for local operation
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation
• CPC Class Codes: Y10S 707/99943 Generating database or data structure, e.g. via user interface
• CPC Class Codes: Y10T 436/11 Automated chemical analysis

Abstract

A system and methods for integrating laboratory instrumentation and applications to provide a unified control and coordination architecture under a common interface. The system provides mechanisms for detection of various hardware and software components wherein the individual functionalities and input/output data types for each component are automatically recognized and incorporated into a centralized control system that provides live monitoring of the operational status of available components.

Claims

1. A control and communications system for a biological laboratory having at least one sample analyzer and a biological data processor, the system comprising:

a client component having a user interface that allows a user to gain access and control or monitor the operation of a plurality of biological instruments in the biological laboratory;

a plurality of instrument components associated with each of the plurality of biological instruments, wherein the plurality of instrument components include an instrument component for the at least one sample analyzer that receives commands selected from at least one pre-set list of commands from the client component and translates the commands into a format that induces the at least one sample analyzer to obtain identification information about a biological sample, wherein the plurality of instrument components further include an instrument component for the biological data processor that receives commands selected from the at least one pre-set list of commands from the client component and translates the commands into a format that induces the biological data processor to analyze the identification information obtained by the at least one sample analyzer and provides signals indicative of the analysis;

at least one directory that provides information to the client component as to the logical location of the plurality of instrument components such that the client component can determine how to access the plurality of instrument components by reference to the at least one directory, wherein the at least one directory includes information about the at least one pre-set list of commands that the client component can use to send signals to the plurality of instrument components to induce the sample analyzer to obtain the identification information and to induce the biological data processor to analyze the identification information;

a messaging service that transmits messages to and from the plurality of instrument components and the client component in a standardized format wherein the messaging service, the at least one directory and the client component are configured such that an additional instruments can be added to the laboratory by associating an instrument component with the additional instrument and updating the at least one directory with information about the logical location of the additional instrument component associated with the additional instrument so that the client component can become aware of the additional instruments by accessing the at least one directory.

2. The system of claim 1, wherein the instrument component for the at least one sample analyzer comprises a component for a sequence analyzer or bioinformatics platform that analyzes DNA, RNA or protein constituents of biological samples.

3. The system of claim 1, wherein the instrument component for the biological data processor comprises a component for a biological data processor that performs one or more of the following functions:

single nucleotide polymorphism analysis, structural analysis, and homology analysis.

4. The system of claim 1, wherein the plurality of instrument components further includes instrument components for at least one thermal cycler.

5. The system of claim 1, wherein the plurality of instrument components further includes instrument components for at least one robot, the robot equipped to locate and physically transfer biological samples.

6. The system of claim 1, further comprising:

at least one instrument type server that is associated with a specific instrument type and which responds to a set of pre-defined instrument type commands by providing data which describe instrument parameters; and

wherein the at least one directory contains information identifying each of the plurality of biological instruments, and information identifying the type and logical address of the at least one instrument type server.

7. The system of claim 6, wherein the at least one directory responds to a request by the client component for information about a requested instrument or instrument type server with a response containing a logical address for at least one instrument component associated with the requested instrument or for the instrument type server so that the client can utilize the logical address to communicate with the at least one instrument component or instrument type server via the messaging service.

8. The system of claim 7, wherein the client component assigns a duty of the requested instrument at a high-level without having to worry about the instrument-specific details of the instrument wherein such details are provided by the at least one directory.

9. The system of claim 6, wherein:

the information contained in the at least one directory identifying each of the plurality of biological instruments includes information identifying one or more of the following;

instrument type, instrument groups, unique instrument serial numbers, instrument availability, and physical locations for instruments;

and the at least one directory provides at least some of this information to the client component in response to a request by the client component to thereby permit a user to evaluate the available instrument in the biological laboratory.

10. The system of claim 6, wherein:

the information contained in the at least one directory identifying each of the plurality of biological instruments includes a list of topics under which messages can be published by at least one instrument component associated with each biological instrument;

the messaging service allows at least one user-interfaced clients to register to receive all messages published by the at least one instrument component that correspond to a topics selected by the client component; and

the messaging service responds to a publication request for a message under an associated topic from the at least one instrument component by sending the message to each of the at least one user-interfaced clients that registered to receive messages under that topic.

11. The system of claim 6, wherein:

the at least one directory implements the Java Naming and Directory Interface;

the messaging service implements the Java Messaging service;

each pre-set list of commands comprises a pre-defined Java interface; and

the set of pre-defined instrument type commands comprises a predefined Java interface.

12. The system of claim 11, wherein each instrument component implements at least one interface whose enumerated methods provide for one or more of the following:

control for a biological instrument by implementing the predefined instructions, receiving instrument status information, receiving instrument history information, and transmitting container and assay information to an instrument.

13. The system of claim 12, wherein each instrument component comprises a plurality of software modules, including:

a state model module, which maintains an instrument state that corresponds to a pre-defined general instrument state model, wherein the at least one interface implementing pre-set commands contains a plurality of commands for causing transitions within the state model; and

a translation module, which translates commands received via the at least one interface implementing commands for causing transitions within the state model and translates these commands into commands which are understood by the instrument hardware.

14. The system of claim 6, wherein the data which describe instrument parameters that is provided by each of the at least one instrument type server includes data describing container and assay parameters and data describing manual control parameters for all instruments of the instrument type associated with the instrument type server.

15. The system of claim 14, wherein the data which describe instrument parameters that is provided by each of the at least one instrument type server comprises XML data corresponding to at least one pre-defined schema.

16. The system of claim 14, wherein:

at least one pre-set list of commands implemented by an instrument component associated with a biological instrument includes a manual control command which takes pre-defined command lines and parameters as input and directly controls the biological instrument hardware based on the commands and parameters; and

the pre-defined command lines and parameters are provided by an instrument type server associated with the instrument to which the manual control command is associated.

17. The system of claim 1, wherein the at least one directory is configured to include information about software applications being used in the system and wherein addition of a new application to the system can be facilitated by updating the at least one directory to include information about the new application thereby allowing the new application to be integrated into the system.

18. The system of claim 1, wherein the system is configured to provide a hardware sharing layer that allows simultaneous connection to an instrument having a limited number of access ports by multiple clients.

19. The system of claim 18, wherein the hardware sharing layer supports Java and non-Java based clients.

20. The system of claim 18, wherein the hardware sharing layer supports web-browser based connectivity.

21. The system of claim 18, wherein the hardware sharing layer allows one connected client to be informed of the activity of another connected client.

22. The system of claim 18, wherein the hardware sharing layer is configured to provide a deliverable communications implementation in the absence of a full data collection infrastructure.

23. The system of claim 18, wherein the hardware sharing layer is configured to be substantially independent of underlying communications layers and instrument specific implementations so as to provide for improved compatibility and flexibility.

24. A method of controlling the operation of a biological laboratory, the method comprising:

associating an instrument component with a biological sample analyzer wherein the instrument component is configured to translate instructions received by the biological sample analyzer so that the biological sample analyzer can be instructed to capture identification information about a biological sample and further,

associating the instrument component with a biological data processor wherein the instrument componenet is configured to translate instructions received by the biological data processor so that the biological data processor can be instructed to analyze identification information captured by the biological sample analyzer;

maintaining a directory for the logical location of each of the instrument components within the biological laboratory such that a user interface can be configured to determine how to access an instrument to implement a process using the directory; and

wherein an additional instrument may be added to the biological laboratory by associating a suitable instrument component to the additional instrument and updating the directory as to the logical location of the instrument component such that the additional instrument can be discovered and accessed by the user interface to implement a process by using the directory.

25. The method of claim 24, further comprising maintaining in the directory of logical locations information for each of the instrument components within the biological laboratory such that the user interface can determine by accessing the directory which of at least one pre-set list of instructions are implemented by each instrument component so that the user interface can access an instrument to implement a process.

26. The method of claim 25, wherein the instrument to be accessed during the implementation of the process is assigned to the process at the beginning of the process.

27. The method of claim 25, wherein the instrument to be accessed during the implementation of the process is selected from one or more of similar instruments after the commencement of the process.

28. The method of claim 27, wherein the selection of the instrument is performed just prior to the access of the instrument, thereby improving the manner in which resources are utilized.

29. The method of claim 25, further comprising transmitting signals between the user interface and the instrument components using the at least one pre-set list of instructions which are then translated by the instrument component and provided to the instrument to thereby control the instrument.

30. The method of claim 29, wherein associating the instrument component comprises drafting a translation process to translate a standard set of instructions into instructions that the instrument is pre-programmed to implement.

31. The method of claim 24, wherein the biological sample analyzer can be instructed to analyze DNA, RNA or protein constituents of biological samples.

32. The method of claim 24, wherein the biological data process can be instructed to perform one of the following functions:

single nucleotide polymorphism analysis, structural analysis, and homology analysis.

33. The method of claim 24, further comprising maintaining at least one set of instrument type information such that the user interface can determine instrument type parameters by accessing a server where the type information is maintained through a pre-set list of instrument type commands.

34. The method of claim 33, further comprising responding to a request by the user interface for information about a requested instrument or instrument type with a response containing a logical address for at least one instrument component associated with the requested instrument or with a logical address for a server containing a set of instrument type information for the requested type so that the user interface can access the requested instrument or instrument type information through a messaging service.

35. The method of claim 34, wherein responding to the request by the user interface allows the user interface to manage the instrument at a high-level without having to worry about the instrument-specific details of the instrument wherein such details are provided by the directory.

36. The method of claim 33, wherein determining instrument type parameters comprises receiving XML data corresponding to at least one pre-defined schema describing instrument type parameters.

37. The method of claim 24, further comprising transmitting a signal to the user interface to indicate that an additional instrument is available in the biological laboratory.

39. The method of claim 24, wherein the directory is configured to include information about software applications being used and wherein addition of a new application can be facilitated by updating the directory to include information about the new application thereby allowing the new application to be integrated.

38. The method of 24, further comprising:

maintaining in the directory of information for each instrument a list of topics under which message will be published by at least one instrument component associated with each instrument;

registering the user interface with a messaging service such that the user interface can receive all messages published by an instrument component that correspond to topics selected by the user interface; and

transmitting messages under a listed topic name to the messaging service so that the messages will be sent to every user interface that registered to receive messages under the listed topic.