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Exploring the new AWS Compute Cluster EC2 Instances
Note: Depending on how you found this post, it might be helpful to understand our own personal & professional biases. We are bioinformatics and HPC types specializing in life sciences, not people trying to build the next twitter or facebook. What we care about when it comes to AWS performance may not be what YOU [...]
Slides from the Amazon Web Services Genomics meeting
I had the unenviable task of giving the first talk after James Hamilton presented the opening keynote at the Amazon Web Services Genomics meeting James is one of the very very few people writing and talking in public about the sorts of things the mega internet scale companies are doing to drive costs down and [...]
WikiLIMS and Toxicogenomics
Stephen Edwards was kind enough to provide his talk slides from his “Wiki-Based Data Management System for Toxicogenomics” presentation at the 2010 Bio-IT-World Conference & Expo. Click on the graphic below to download the PDF formatted version of his presentation.
CHI XGEN Short Course Slides
As promised, here are the PDF talk slides from the sessions presented at our Short Course on Data Management Strategies for Next-Generation DNA Sequencing — part of the XGEN Congress held in San Diego.
Supporting Haiti
On Friday the 29th of January, I will be taking a week’s leave of absence from my day to day responsibilities at Bioteam and traveling to Haiti with a medical relief team. I’ll be going with a group called Family Health Ministries. We’ll go overland through the Dominican Republic to a clinic where my wife [...]
Maximizing Utility on the Cloud
For the 2009 BioIT World Conference in Europe I was invited with short notice to give a 60 minute talk centering on practical Cloud approaches for life science organizations. The talk was not really technical in nature and had to hit a huge number of topic areas as well. Overall feedback was positive and a [...]
Storage for Next-Gen Sequencing
Presenter slides from the 2009 Storage for Next-Generation Sequencing Workshop(s)
Antibody Docking in the Amazon Cloud
Adam Kraut has written up his experiences with a Pfizer protein docking experiment on Amazon AWS in a recent BioIT World column: “… The new docking architecture at Pfizer employs nearly the entire suite of services offered by Amazon. A huge array of Rosetta workers can be spun up on EC2 by a single protein [...]
Instead of spending 20 minutes to format an ext3 volume every time you need one, you could just snapshot a ...
Let me add a few remarks about Ext3 as well.
The reason we usually recommend Ext3 instead of XFS is because ...
I'm using these slides to tune SGE 6.2 @ European Space Agency, thanks a lot! 
Great post.
Can you also try our native scale out NFS protocol? Next 3.1 release of Gluster will include it ...
So far my mental architecture is shaping up to be something like this:
Use the ephemeral disks for scratch space and ...
This shows that on-demand HPC still has a ways to go, it is very unfortunate that only ext3 is supported ...
We have had sge62u3 working fine in a 10.5 cluster using cron to startup the sge_execd process on clients. Trying ...
Instead of increasing your disk image size, you could have decreased the memory by writing a very short C program ...