Biological data networks and methods therefor

• US 9,215,162 B2
• Filed: 03/09/2012
• Issued: 12/15/2015
• Est. Priority Date: 03/09/2011
• Status: Active Grant

• Current Assignee: Sala, Inc.
• Original Assignee: Annai Systems Inc
• Inventors: Ganeshalingam, Lawrence, Allen, Patrick Nikita
• Primary Examiner(s): WONG, XAVIER S
• Application Number:
  US13/417,192
• Publication Number:
  US 20120230339A1
• Time in Patent Office: 1,376 Days
• US Class Current: 1/1
• CPC Class Codes: G06F 2209/484 Precedence
• CPC Class Codes: G06F 9/52 Program synchronisation; Mutual exclusion, e.g. by means of semaphores
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: H04L 45/00 Routing or path finding of packets in data switching networks routing or path finding in wireless networks H04W40/00

Abstract

A system and method of transmitting and receiving information pertaining to biological sequence data is disclosed. The method includes receiving, at a network interface of a node of a network, a data packet including a first header containing network routing information and a second header associated with a layered model representative of the biological sequence data. The method also includes parsing the data packet and separating the first header from the second header.

Claims

1. A network node, comprising:

a data container including a plurality of biological data units, each of the plurality of biological data units including;

a payload containing biological sequence data,

a first BioIntelligent™

header associated with biological information relating to biological sequence data wherein the first BioIntelligent™

header identifies a first biological characteristic associated with a first subset of the biological sequence data, and

a second BioIntelligent™

header identifying a second biological characteristic associated with a second subset of the biological sequence data;

a processor configured to identify, in response to a query received by the network node, at least one of the first BioIntelligent™

header and the second BioIntelligent™

header associated with a first of the plurality of biological data units wherein the first of the plurality biological data units includes first sequence data;

a packet generator configured to generate a data packet associated with the first sequence data, the data packet including a first header containing network routing information relating to a network communications protocol and a second header associated with a layered model different from the network communications protocol wherein the layered model is representative of the biological sequence data and wherein the second header is the at least one of the first BioIntelligent™

header and the second BioIntelligent™

header and is different from the first sequence data;

a queue communicatively coupled to the packet generator, the queue storing the data packet; and

a transmit controller for controlling transmission of the data packet to a node of a network.

2. The network node of claim 1 wherein the packet generator is further configured to generate a third header and wherein the second header is associated with a first layer of the layered model and the third header is associated with a second layer of the layered model.

3. The network node of claim 2 wherein the first layer comprises a DNA-specific layer and the second layer comprises an RNA-specific layer.

4. The network node of claim 3 wherein the second header information pertains to a characteristic of DNA and the third header information pertains to a characteristic of RNA.

5. The network node of claim 3 wherein the packet generator is further configured to generate a fourth header and wherein the fourth header is associated with a third layer of the layered representation of biological sequence data.

6. The network node of claim 5 wherein the third layer comprises a protein-specific layer.

7. The network node of claim 1 wherein the biological sequence data comprises polymeric data.

8. The network node of claim 1 wherein the biological sequence data comprises DNA sequence data.

9. The network node of claim 1 wherein the biological sequence data comprises genomic sequence data.

10. The network node of claim 1 wherein the second header is associated with biological information.

11. The network node of claim 10 wherein the biological information identifies one or more portions of the biological sequence data associated with a disease condition.

12. The network node of claim 11 wherein the biological information comprises one or more characteristics of the biological sequence data.

13. The network node of claim 12 wherein the biological sequence data comprises a segment of DNA sequence data.

14. The network node of claim 13 wherein the one or more characteristics relate to a property of the segment of DNA sequence data.

15. The network node of claim 14 wherein the property comprises a number of exons included within the segment of DNA sequence data.

16. The network node of claim 14 wherein the property comprises locations of exons included within the segment of DNA sequence data.

17. The network node of claim 14 wherein the property relates to an extent of methylation within the segment of DNA sequence data.

18. The network node of claim 14 wherein the property comprises one or more molecular pathways associated with the segment of DNA sequence data.

19. The network node of claim 14 wherein the property relates to one or more gene mutations within the segment of DNA sequence data.

20. The network node of claim 1 wherein the queue includes other data packets to be transmitted.

21. The network node of claim 1 wherein the generating further includes generating a third header containing metadata associated with a different subset of the sequence data.

22. The network node of claim 1 wherein the generating the third header includes identifying an additional biological characteristic associated with the subset of the sequence data wherein a biological relationship exists between second header information included within the second header and third header information included within the third header.

23. A network node, comprising:

a data container including a plurality of biological data units, each of the plurality of biological data units including;

a payload containing biological sequence data,

a first BioIntelligent™

header associated with biological information relating to biological sequence data wherein the first BioIntelligent™

header identifies a first biological characteristic associated with a first subset of the biological sequence data, and

a second BioIntelligent™

header identifying a second biological characteristic associated with a second subset of the biological sequence data;

a processor configured to evaluate, in response to a query received by the network node, headers of the plurality of biological data units in order to identify at least one of the first BioIntelligent™

header and the second BioIntelligent™

header associated with a first of the plurality of biological data units wherein the first of the plurality biological data units includes first sequence data;

a packet generator configured to generate a data packet associated with the first sequence data, the data packet including a first header containing network routing information relating to a network communications protocol and a second header associated with a layered model different from the network communications protocol wherein the layered model is representative of biological sequence data wherein the second header is the at least one of the first BioIntelligent™

header and the second BioIntelligent™

header and is different from the first sequence data;

a queue communicatively coupled to the packet generator, the queue storing the data packet; and

a transmit controller for controlling transmission of the data packet to another node of a network;

a network interface configured to receive a data packet including a first header containing network routing information and a second header associated with a layered model representative of the biological sequence data; and

a processing module communicatively coupled to the network interface, the processing module parsing the data packet and separating the first header from the second header.

24. The network node of claim 23 wherein the queue includes other data packets to be transmitted.

25. The network node of claim 23 wherein the packet generator is further configured to generate a third header containing metadata associated with a different subset of the sequence data.