Tweet
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
Any ideas? Matt
-
-
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. -
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!
Comment
-
I am starting to look into this, I'll let you guys know if I get anywhere.--
Senthil PalanisamiComment
-
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.
Best,
KristenComment
-
-
Hi,
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 http://aws.amazon.com/ec2/pricing/Comment
-
Hi,
If there are enough interests on a user guide on how to get starting with Amazon EC2, I can put one together.
QComment
-
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM -
Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM -
Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...07-08-2026, 05:17 AM
Comment