WTF? Illumina Wants to Patent All Online Bioinformatics Programs !!

Readers may find the following patent application interesting (h/t: @genetics_blog).

Cloud computing environment for biological data

Someone should tell the Illumina’s IP lawyers that ‘cloud computing’ is a buzzword to describe the internet. What next? The Onion patenting a method to crack jokes online? Dilbert creator Scott Adams patenting cartoons on silly patent applications and other corporate management decisions? 23 and Me patenting human genetics? (Please note that the last one is a real patent).

Details of Illumina patent application follow.

CLAIMS(20)

1. A system for analyzing biological samples, comprising:

a cloud computing environment in communication with a plurality of sequencing devices, wherein the cloud computing environment comprises at least one server, the server being configured to communicate with a sequencing system remote from the server to receive and store sequence data from the sequencing system while the sequence data is being generated.

2. The system of claim 1, comprising a sequencing module configured to generate the sequence data and a communications module configured to communicate the sequence data to the server.

3. The system of claim 1, wherein the communications module is configured to receive a user instruction related to communicating the sequence data to the cloud computing environment, and wherein a default state of the communications module is to communicate the sequence data to the cloud computing environment in an absence of the user instruction.

4. The system of claim 1, wherein the sequence data comprises data derived from fluorescence intensities.

5. The system of claim 1, wherein the sequence data comprises data derived from base identities of a plurality of nucleotide strands.

6. The system of claim 1, wherein the cloud computing environment comprises at least one processor configured to:

receive the sequence data; and

assemble at least a portion of a genome based on the sequence data.

7. The system of claim 1, wherein the communications module is configured to communicate a user instruction related to analysis of the sequence data using the cloud computing environment, and wherein the sequence data is analyzed by the cloud computing environment based on the user instruction without further instructions by the user.

8. The system of claim 1, wherein the cloud computing environment comprises at least one processor configured to:

receive one or more instructions related to sharing the sequence data from an originator of the sequence data.

9. The system of claim 8, wherein the cloud computing environment comprises at least one processor configured to:

receive a request from a secondary user related to the sequence data;

authenticate the secondary user based on instructions provided by the originator of the sequence data; and

provide the sequence data to the secondary user if the secondary user has permission to access the sequence data.

10. The system of claim 1, wherein the sequence data is stored on the cloud computing environment.

11. The system of claim 1, wherein the sequence data is not stored on the sequencing device after a sequencing run is complete.

12. The system of claim 1, wherein the communications module is configured to distribute the sequence data to a plurality of computer systems connected to the communications module for analysis of the sequence data.

13. The system of claim 12, wherein the cloud based network is configured to determine processing capabilities of computers of the plurality of computer systems, and to distribute the sequence data for analysis based upon the determination.

14. A computer implemented method for analyzing sequence data in a cloud computing environment, comprising:

receiving, at a server, a request from a user to annotate sequence data stored on a cloud computing environment;

determining if the user has permission to annotate the sequence data;

modifying the sequence data based on an instruction related to an annotation if the user has permission to annotate the sequence data; and

storing the sequence data with the annotation.

15. The method of claim 14, wherein the annotation comprises information about the user.

16. The method of claim 14, comprising receiving a request from a secondary user to rate the annotation; and storing a rating of the annotation with the sequence data.

17. The method of claim 16, comprising determining a quality of the annotation based on one or more ratings and removing the annotation if the quality of the annotation is below a threshold.

18. The method of claim 14, wherein determining if the user has permission to annotate the sequence data comprises determining if the user is an owner of the sequence data.

19. The method of claim 14, wherein the annotation is visible only to secondary users that have permission to view the sequence data.

20. A system for analyzing biological samples, comprising:

at least one networked computer system configured to:

receive sequence data from a remote sequencing device, wherein the sequence data comprises permissions for accessing the sequence data;

receive a request from a secondary user to access the sequence data, the secondary user being different from the remote sequencing device; and

allowing the secondary user access to the sequence data if the secondary user is authorized under the permissions.

We still believe Illumina will be better served by firing most of its IP lawyers and tripling the salary of Anthony Cox and alike.

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