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Old 09-18-2009, 10:03 AM   #1
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Location: Durham, NH

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Default Cloud Computing for Assembly?

Is anyone working on this? I am interested in using cloud computing for a de novo Solexa assembly of mammal transcriptome. Looked at Amazon, but they will only dedicate ~15gb RAM per instance/user.

Any ideas? Matt
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Old 09-18-2009, 01:14 PM   #2
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Would it be possible to start up multiple instances and cluster them so they share the RAM? I could be talking rubbish though, as I'm not well versed in EC2 or computing clusters!

There's a test program in the Amazon Elastic Map Reduce called CloudBurst which is supposed to do short read mapping to a reference genome, although I haven't used it, I've only seen the paper. The Amazon info for it is at http://developer.amazonwebservices.c...xternalID=2272.
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Old 09-18-2009, 07:19 PM   #3
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That is pretty cool. I'd love to get together a more complete userguide for launching EC2 instances for beginners (myself included).

I know of another similar cloud project that is getting ready to launch...maybe that time is getting closer!
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Old 09-20-2009, 09:32 PM   #4
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I am starting to look into this, I'll let you guys know if I get anywhere.
Senthil Palanisami
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Old 09-28-2009, 10:43 AM   #5
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Hi Matt,
I've talked to Amazon Web Services and it sounds like a viable option for running a distributed-RAM method like ABySS. Pretty affordable too. They recommended a contractor to me who has experience setting up MPI-enabled jobs on EC2 which would be necessary to do ABySS.

I believe they are also going to get some larger-RAM machines available in the near future.

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Old 10-11-2012, 12:30 AM   #6
Location: chennai

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Just go and try it here erp on cloud
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Old 10-11-2012, 06:36 AM   #7
Location: Canada

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You can use the "High-Memory Quadruple Extra Large Instance" instance type, which comes with 64GB of RAM and costs $1.8 per hour:

For prices, see
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Old 10-11-2012, 06:40 AM   #8
Location: Canada

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If there are enough interests on a user guide on how to get starting with Amazon EC2, I can put one together.

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cloud computing, de novo assembly, rna-seq, solexa, transcriptomes

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