Research system using multi-platform object oriented program language for providing objects at runtime for creating and manipulating biological or chemical data to facilitate research

• US 6,453,333 B1
• Filed: 06/10/1998
• Issued: 09/17/2002
• Est. Priority Date: 06/11/1997
• Status: Expired due to Fees

• Current Assignee: Netgenics Corporation
• Original Assignee: Lion Bioscience AG (2invest AG)
• Inventors: Soclof, Michal S., Glynias, Manuel J., OʼDell, Joanne M., Forsch, Daniel A., Dickson, Michael C.
• Primary Examiner(s): Luu, Le Hien
• Application Number:
  US09/095,083
• Publication Number:
  US 20020029255A1
• Time in Patent Office: 1,560 Days
• Field of Search: 709/202, 709/201, 709/203, 709/217, 709/218, 709/315, 709/219, 707/3, 717/10
• US Class Current: 709/202
• CPC Class Codes: G06F 16/25 Integrating or interfacing systems involving database management systems
• 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: G16B 50/40 Encryption of genetic data
• CPC Class Codes: G16C 20/90 Programming languages; Computing architectures; Database systems; Data warehousing

Abstract

A drug discovery research system which includes a plurality of computers. The drug discovery research system provides for at least one of the plurality of computers to run a multi-platform object oriented programming code, and at least one of the plurality of computers to store drug discovery related data. The system has a network architecture interconnecting the plurality of computers. The network architecture allows objects to transparently communicate with each other. The drug discovery research system provides for integrating and organizing data to facilitate drug discovery research.

Claims

1. A framework to facilitate at least one of bioinformatics and chemi-informatics research, comprising:

a plurality of computers, at least one of the plurality of computers running a multi-platform object oriented programming code, and at least one of the plurality of computers storing at least one of biological and chemical data, the computer storing the data providing the computer running the object oriented programming code with program data at run time to enable at least one of creation, manipulation, and viewing of the data, at least one of the plurality of computers being operative as a server, the server providing to the computer running the object oriented programming code a list at run time identifying services available to the server, the list representing objects by class name and the computer running the object oriented programming code being operable to invoke at least one of the services by class name based on the list, thereby causing the server to instantiate corresponding class objects by name at run time; and

a network architecture interconnecting the plurality of computers, the network architecture allowing objects to transparently communicate with each other;

whereby the framework provides for integrating and organizing the data to facilitate at least one of biological and chemical research.

2. The framework of claim 1, further comprising means for dynamically swapping operations performed by the computer storing the data with operations performed by the computer running the object oriented programming code.

3. The framework of claim 1, wherein the computer storing the data is operable as the server for the framework.

4. The framework of claim 3, wherein the classes are Java client classes having objects that are instantiated by name at run time to implement Common Object Request Broker Architecture client interfaces to changing server components.

5. The framework of claim 1, wherein the framework organizes the data to perform DNA sequence analysis.

6. The framework of claim 1, wherein the framework organizes the data to perform chemical analysis.

7. The framework of claim 1, wherein a groupware framework is provided around a distributed object model wherein a client is extensible in real time and downloads as a client object.

8. The framework of claim 7, wherein the groupware framework further comprises an annotated collaborative framework, wherein at least two users can concurrently work on different portions of a document object in real-time.

9. The framework of claim 6, wherein the groupware framework further comprises a screen sharing collaborative framework, wherein at least two users of the can concurrently screen share an instance of an object in real-time, the instance of the object running on one of the plurality computers.

10. The framework of claim 7, wherein the groupware framework further comprises an annotated collaborative framework in which at least two users of the system can concurrently work on different portions of a document object in real-time.

11. The framework of claim 10, wherein each user sharing the document object in the collaborative framework is dynamically assigned different portions of the document object so as to inhibit multiple users from concurrently modifying the same portion of the document object.

12. The framework of claim 1, wherein the server provides the computer running the object oriented programming code with an updated list of objects to reflect a change to the list of objects available to the server.

13. A framework to facilitate research, comprising:

at least two computers, including a first computer and a second computer, the first computer running multi-platform object oriented programming code and storing vertical market data, the first computer providing to the second computer a list at run time, the list identifying by class name services available to the first computer, the second computer being operable to invoke at least one of the services by class name based on the list causing the first computer to instantiate corresponding class objects by class name at run time; and

a network architecture operatively coupling the at least two computers, the network architecture allowing objects to transparently communicate with each other and affording the second computer access to the object oriented programming code and the stored data;

whereby the framework provides for integrating and organizing the data to facilitate research

wherein the framework organizes the data to perform DNA sequence analysis.

14. An informatics research system, comprising:

a server computer for carrying out operations in connection with the system, the server computer being operatively coupled to a network backbone;

at least one client computer for providing user access to the informatics research system, the at least one client computer being operatively coupled to the network backbone; and

the client computer having zero footprint access to a plurality of software applications and informatics data via the server computer, and the server sending the at least one client computer a list at run time identifying services available to the server computer, the list representing class objects by class name and the client computer being operable to invoke a service by class name based on the list and cause the server to instantiate a corresponding class object by name at run time;

the client computer including item classes which represent views of data residing on the server computer, the item classes including a DNA sequence item, and the client computer serving as a view manager of persistent data residing on the server computer.