METHODS AND SYSTEMS FOR USING A CLOUD COMPUTING ENVIRONMENT TO SHARE BIOLOGICAL RELATED DATA

• US 20140214579A1
• Filed: 03/08/2013
• Published: 07/31/2014
• Est. Priority Date: 01/25/2013
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Shen, Min-Jui Richard, Lin, Charles Hsuan
• Granted Patent: US 9,805,407 B2
• Time in Patent Office: Days
• US Class Current: 705/26.1
• CPC Class Codes: G06Q 30/0601 Electronic shopping [e-shopping]
• CPC Class Codes: G06Q 30/0609 Buyer or seller confidence or verification
• CPC Class Codes: G06Q 30/0621 Item configuration or customization
• CPC Class Codes: G06Q 30/0627 using item specifications
• CPC Class Codes: G06Q 30/0635 Processing of requisition or of purchase orders
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/10 Ontologies; Annotations
• 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

Abstract

The present disclosure provides a novel approach for shifting or distributing various information (e.g., protocols, analysis methods, sample preparation data, sequencing data, etc.) to a cloud-based network. For example, the techniques relate to a cloud computing environment configured to receive this information from one or more individual sample preparation devices, sequencing devices, and/or computing systems. In turn, the cloud computing environment may generate information for use in the cloud computing environment and/or to provide the generated information to the devices to guide a genomic analysis workflow. Further, the cloud computing environment may be used to facilitate the sharing of sample preparation protocols for use with generic sample preparation cartridges and/or monitoring the popularity of the sample preparation protocols.

Claims

1. A computer-implemented method for sharing and monitoring use of protocols for preparing biological samples using generic sample preparation cartridges in a cloud computing environment, comprising:

receiving from a submitter, at a server, a protocol for sample preparation using a generic sample preparation cartridge on the cloud computing environment;

monitoring for a request from a requester for the protocol or for a use of the protocol; and

crediting the submitter with a purchase credit from a supplier of the generic sample preparation cartridge for at least one request for the protocol or use of the protocol.

2. The method of claim 1, comprising receiving from the requester, at the server, a request for the protocol.

3. The method of claim 2, comprising providing to the requester the protocol or the protocol and an analysis method for use with the protocol.

4. The method of claim 3, comprising receiving a rating for the protocol from the requester.

5. The method of claim 1, comprising receiving from the submitter, at the server, an analysis method for use with the protocol.

6. The method of claim 1, comprising receiving from the supplier, at the server, a validation of the protocol.

7. The method of claim 1, comprising receiving, at the server, a citation of a publication that cites, uses, or both cites and uses the protocol.

8. The method of claim 1, comprising conferring a certified status to the protocol based on a number of requests for the protocol by requesters, ratings of the protocol by the requesters, a number of citations for the protocol, validation of the protocol, or a combination thereof.

9. The method of claim 8, comprising conferring a supplier supported status to the protocol, wherein the protocol is utilized with an application-specific sample preparation cartridge designed by the supplier based on the protocol.

10. A system for sharing and monitoring use of protocols for preparing biological samples using generic sample preparation cartridges, comprising:

a cloud computing environment in communication with a plurality of computer systems, wherein the cloud computing environment comprises at least one server and at least one processor, the at least one server being configured to communicate with at least one of the computer systems to receive and store a protocol for sample preparation using a generic sample preparation cartridge, and the at least one processor being configured to monitor for a request by a requester for the protocol and to credit a submitter of the protocol with purchase credit from a supplier of the generic sample preparation cartridge for at least one request for the protocol.

11. The system of claim 10, wherein the at least one server is configured to receive a request for the protocol from the requester.

12. The system of claim 11, wherein the at least one server is configured to provide to the requester the protocol or the protocol and an analysis method for use with the protocol.

14. The system of claim 10, wherein the at least one server is configured to receive from the submitter an analysis method for use with the protocol.

15. The system of claim 10, wherein the at least one server is configured to receive from the supplier a validation of the protocol.

16. The system of claim 10, wherein the at least one server is configured to receive a citation of a publication that cites, uses, or both cites and uses the protocol.

17. The system of claim 10, wherein the at least one processor is configured to confer a certified status to the protocol based on a number of requests for the protocol by requesters, ratings of the protocol by the requesters, a number of citations for the protocol, or a combination thereof.

18. The system of claim 17, wherein the at least one processor is configured to confer a supplier supported status to the protocol, wherein the protocol is utilized with an application-specific sample preparation cartridge designed by the supplier based on the protocol.

19. The system of claim 18, wherein the at least one server is configured to receive instructions from the supplier to confer the supplier supported status to the protocol.

13. The system of claim 13, wherein the at least one server is configured to receive a rating for the protocol from the requester.

20. A system for sharing and monitoring use of protocols for preparing biological samples using generic sample preparation cartridges, comprising:

a cloud-based server in communication with a plurality of computer systems;

a memory component that receives, via the server, protocols for sample preparation using generic sample preparation cartridges and stores the protocols; and

a processor configured to;

receive requests for one or more of the protocols;

monitor a number of requests or uses for each of the protocols; and

credit a submitter of a respective protocol with a purchase credit from a supplier of the generic sample preparation cartridges for at least one request for the respective protocol or use of the respective protocol.