Cloud computing environment for biological data

• US 10,223,502 B2
• Filed: 09/07/2016
• Issued: 03/05/2019
• Est. Priority Date: 04/11/2012
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Dickinson, Alexander G., Garcia, Francisco Jose, Kain, Robert C., Kahn, Scott D., Nelson, Andrew R.
• Primary Examiner(s): Serrao, Ranodhi
• Application Number:
  US15/258,651
• Publication Number:
  US 20160378940A1
• Time in Patent Office: 909 Days
• CPC Class Codes: G06F 21/6218 to a system of files or objects, e.g. local or distributed file system or database
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• 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: G16B 50/30 Data warehousing; Computing architectures
• 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: G16H 40/67 for remote operation
• CPC Class Codes: H04L 63/08 for authentication of entities cryptographic mechanisms or cryptographic arrangements for entity authentication H04L9/32
• CPC Class Codes: H04L 63/102 Entity profiles
• CPC Class Codes: H04L 67/10 in which an application is distributed across nodes in the network software deployment G06F8/60; multiprogramming arrangements G06F9/46

Abstract

The present invention provides a novel approach for storing, analyzing, and/or accessing biological data in a cloud computing environment. Sequence data generated by a particular sequencing device may be uploaded to the cloud computing environment during a sequencing run, which reduces the on-site storage needs for the sequence data. Analysis of the data may also be performed in the cloud computing environment, and the instructions for such analysis may be set at the originating sequencing device. The sequence data in the cloud computing environment may be shared according to permissions. Further, the sequence data may be modified or annotated by authorized secondary users.

Claims

1. A computer implemented method in a cloud computing environment, comprising:

receiving, in a cloud computing environment, sequence data generated by a sequencing device performing sequencing runs;

receiving, in the cloud computing environment, device diagnostic data relating to a condition of the sequencing device and comprising information about a number of the sequencing runs performed by the sequencing device;

storing the sequence data and the device diagnostic data in the cloud computing environment;

communicating a message to an authorized user of the sequencing device based on the sequencing runs, wherein the message is a reagent supply reminder based on the number of the sequencing runs; and

communicating, from the cloud computing environment, the device diagnostic data to a manufacturer of the sequencing device.

2. The method of claim 1, wherein the message further comprises a maintenance reminder for the sequencing device based on the number of the sequencing runs.

3. The method of claim 1, wherein the device diagnostic data comprises information about a bug or error in the sequencing device.

4. The method of claim 1, wherein the device diagnostic data comprises information about a software update check.

5. The method of claim 4, comprising determining that the sequencing device needs a software update and communicating the software update to the sequencing device.

6. The method of claim 1, wherein the device diagnostic data is received together with the sequence data by the cloud computing environment.

7. The method of claim 1, wherein the sequence data comprises base calls.

8. The method of claim 1, wherein the sequence data comprises quality data.

9. The method of claim 8, wherein message is further based on the quality data.

10. The method of claim 1, wherein the authorized user is a laboratory facility.

11. The method of claim 1, wherein the device diagnostic data does not comprise the sequence data.

12. A sequencing device, comprising:

an imager configured to acquire image data from a sequencing reaction;

a processor configured to execute instructions to;

receive a user input related to one or more parameters of the sequencing reaction;

receive a user input related to a permission to communicate sequence data to be generated from the image data of the sequencing reaction to a cloud computing environment;

generate the sequence data from the image data;

communicate device diagnostic information relating to the sequencing device to the cloud computing environment, wherein a manufacturer of the sequencing device is an authorized user of the device diagnostic information and not of the sequence data, wherein the device diagnostic information comprises information about a software update check; and

determine that the sequencing device needs a software update and communicate the software update to the sequencing device; and

a memory storing the instructions.

13. The sequencing device of claim 12, wherein the processor is further configured to execute instructions to:

perform a diagnostic check to generate the device diagnostic information.

14. The sequencing device of claim 13, wherein the diagnostic check is a check for bugs or errors.

15. The sequencing device of claim 12, wherein the device diagnostic information comprises a number of sequencing runs performed by the sequencing device.

16. The sequencing device of claim 12, wherein the device diagnostic information comprises the one or more sequencing parameters.

17. A method, comprising:

generating sequence data using a sequencing device using an imager configured to acquire image data from a sequencing reaction to generate the sequence data;

receiving a user input related to one or more parameters of the sequencing reaction;

receive a user input related to permissions;

communicating the sequence data to a cloud computing environment;

communicating the permissions to the cloud computing environment, wherein the permissions define a set of authorized users for the sequence data and for diagnostic information of the sequencing device;

communicating the device diagnostic information of the sequencing device to the cloud computing environment, wherein a manufacturer of the sequencing device is an authorized user of the device diagnostic information and not of the sequencing data, wherein the device diagnostic information comprises information about a software update check; and

receiving a software update at the sequencing device based on the software update check.

18. A method, comprising:

receiving, in a cloud computing environment, sequence data and device diagnostic data from a sequencing device;

receiving, in a cloud computing environment, permissions for the sequence data, wherein the permissions define a set of authorized users for the sequence data; and

communicating, from the cloud computing environment, device diagnostic information of the sequencing device to a manufacturer of the sequencing device, wherein the device diagnostic data comprises information about a number of sequencing runs performed by the sequencing device; and

communicating a reagent supply reminder message to an authorized user of the set of authorized users of the sequencing device based on the number of sequencing runs.

19. The method of claim 18, wherein the device diagnostic data does not comprise the sequence data.