Hey guys,
So we're a startup bioinformatics lab. We have a "workstation" running 2x E5-2650 v2s and 128GB ram. So essentially it's a down-stream analysis machine. We're working with transcriptomes roughly around 30-70k genes in size.
Right now we have been doing as much on the cloud as we can. Locally we have only cleaned our raw reads and assembled on iPlant or Galaxy public servers. We do want to add a capability to do the assembly locally.
Right now our limiting step is the Blastx process. Splitting the assembled fasta file into 10 smaller fragments, we can run all 10 at once and have the completed sequence finished in roughly 15 days.
Now:
We have obtained around 8500 dollars for an increase to our current computational power. What I'm thinking is obtaining some off-lease, refurbished blade systems from eBay or another retailer like Xbyte. If we do go this route, a quick eBay search brought me to setups similar to these few items:
In your professional opinion, how much of an upgrade would these systems be if we build a cluster using this setup? Would we be able to significantly cut down on our Blast time, if we can dedicate more cores/break-up the fasta file into smaller segments?
Thank you for your feedback!
So we're a startup bioinformatics lab. We have a "workstation" running 2x E5-2650 v2s and 128GB ram. So essentially it's a down-stream analysis machine. We're working with transcriptomes roughly around 30-70k genes in size.
Right now we have been doing as much on the cloud as we can. Locally we have only cleaned our raw reads and assembled on iPlant or Galaxy public servers. We do want to add a capability to do the assembly locally.
Right now our limiting step is the Blastx process. Splitting the assembled fasta file into 10 smaller fragments, we can run all 10 at once and have the completed sequence finished in roughly 15 days.
Now:
We have obtained around 8500 dollars for an increase to our current computational power. What I'm thinking is obtaining some off-lease, refurbished blade systems from eBay or another retailer like Xbyte. If we do go this route, a quick eBay search brought me to setups similar to these few items:
In your professional opinion, how much of an upgrade would these systems be if we build a cluster using this setup? Would we be able to significantly cut down on our Blast time, if we can dedicate more cores/break-up the fasta file into smaller segments?
Thank you for your feedback!
Comment