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AN OVERBROAD PATENT ON DNA Analytics in the cloud - This application from Illumina seeks to patent the idea of...DNA analysis done by a server which is remote to the DNA sequencer! 10 minutes of your time can help narrow US patent applications before they become patents. Follow @askpatents on twitter to help.

QUESTION - Have you seen anything that was published before 4/11/2012 that discusses:

  • Separating the DNA analysis in the cloud from the DNA sequencer in the lab

If so, please submit evidence of prior art as an answer to this question. We welcome multiple answers from the same individual.

EXTRA CREDIT - DNA sequencing with standard fluorescent nucleotides but where server is remote to the sequencing machine

TITLE: Cloud-based DNA sequencing analysis

Summary: [Translated from Legalese into English] Connecting a cloud computing environment to multiple DNA sequencers and doing DNA analysis in the cloud (remote from the sequencers).

  • Publication Number: US 20130275486 A1
  • Application Number: US 13/790,596
  • Assignee: Illumina
  • Prior Art Date: Seeking prior Art predating 4/11/2012
  • Open for Challenge at USPTO: Open through 4/15/2014
  • Link to Google Prior Art Search - "Find Prior Art"

Claim 1 requires each and every step below:

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.

In English this means:

A system for analyzing biological samples, comprising:

A cloud computing environment communicating with multiple sequencing devices, where

The cloud computing servers communicate with a remote sequencing system to receive and store sequence data while the sequence data is being generated.

Good prior art would be evidence of a system that did each and every one of these steps prior to 4/11/2012

You're probably aware of ten pieces of art that meet this criteria already... separately, the applicant is claiming Cloud-based sequence analysis which uses multiple, distributed networks of computers to do the analysis

"Method of providing sequence data to the cloud computing environment" from the Applicant

A first example of prior art is www.dnanexus.com, which has been offering this solution since 2010.

What is good prior art? Please see our FAQ.

Want to help? Please vote or comment on submissions below. We welcome you to post your own request for prior art on other questionable US Patent Applications.

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  • Thanks for participating in Ask Patents. I have updated this prior art request to add additional information and conform to the Prior Art Request Template at Ask Patents. Feel free to edit or correct any mistakes on my side. Thanks. Also, please add your first piece of prior art as an answer below. (It's fine to answer your own question on Ask Patents)
    – Micah Siegel
    Commented Nov 21, 2013 at 0:17
  • This is pretty specific, so there may not be great prior art. Isn’t it kind obvious, though?
    – Kevin Chen
    Commented Nov 21, 2013 at 1:14
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    The patent office can't go by "seems obvious". They find the closest documented prior work and if that does not have everything required they find other prior work to fill in all the holes and then need to explain why someone would walk up one morning and put them all together. Otherwise most everything seems obvious after you hear it.
    – George White ♦
    Commented Nov 21, 2013 at 1:19
  • "The cloud" is similar to what used to be called a server farm. Google came up with this: kurzweilai.net/…
    – jdv-Jan de Vaan
    Commented Nov 22, 2013 at 19:06
  • Cloud computing is a marketing name and synonym for a shared server or group of shared servers. As such, the University of Oklahoma's Human Genome Sequencing labs were doing such sequencing on internal "cloud" servers back in 2001. You may want to consider investigating that avenue further. genome.ou.edu
    – John S.
    Commented Jan 3, 2014 at 18:47

3 Answers 3

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Cloud BioLinux http://www.ncbi.nlm.nih.gov/pubmed/22429538

Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms.

Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud

Galaxy NGS IS (probably too new) http://www.ncbi.nlm.nih.gov/pubmed/23479349

the platform provides the researcher with a user-friendly interface to create a request, submit accompanying samples, upload sample quality measurements and access to the sequencing results

As this is using the Galaxy platform and Galaxy can be easily run in the cloud via the Cloudman it should be relevant.

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  • Answers with stand-alone content rather than mostly just a link are preferred on all stack exchange sites, including ask patents.
    – George White ♦
    Commented Dec 23, 2013 at 5:33
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Perhaps not entirely on-target, but Genome@Home was active at least as far back as 2001:

The latter link includes the following references:

Larson SM, Snow CD, Shirts MR, Pande VS. (2003) "Folding@Home and Genome@Home: Using distributed computing to tackle previously intractable problems in computational biology." to appear in Computational Genomics, Richard Grant, editor, Horizon Press [pdf]

Talk: March 2001, Carleton University Biochemistry & Chemistry Society, Ottawa, ON. "Folding@home and Genome@home: Protein folding and design with distributed computing." [ppt]

So the idea of using remote computers for analysis is not new; though the direct (or semi-direct) connection of sequencers to those remote computers is not covered by this.

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While not directly answering the question, then this may give you pointers for where to get more information...

Jason Hoffman who was the CTO for Joyent (a San Francisco based cloud company) always cited his motivations for founding Joyent as having a cloud environment for DNA research.

http://gigaom.com/2012/10/12/how-jason-hoffman-helped-save-his-moms-life-and-along-the-way-came-up-with-a-new-way-to-build-computers/

In 2005, Hoffman’s mother was diagnosed with breast cancer. [....] it combined research on specific cancers with genetic analysis on his mom. That genetic analysis required a lot of computing power [...] supplied with his hosting company, Joyent.

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