What’s the Answer? (hardware help)

BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

There’s a range of topics that come up at Biostar. But there are some that I find particularly suited to this kind of community discussion that can be hard to find from other places. When you are talking to hardware vendors, they may have good information–but they may prefer to guide you towards pieces that aren’t so right for your anticipated needs. This week someone needs some guidance on hardware setup for crop plant genomics. If you have any insight on this, please help out.

Question: Hardware for Crop NGS data tools

We are creating a specification for a new server for our research scientists in applied genetics and breeding (I am a computer scientist).

Any advice regarding the number of processors/cores and RAM would be most helpful. Here is a background to the work being carried out, kindly written by a colleague of mine:

[list of stuff they do, go see it over there]

Unfortunately, the budget is small for the server itself – approximately £10,000 (~ 16,000 USD), though it could be increased if it is not enough to work with. Some of the servers I have looked at offer 256GB of RAM. Would this be enough to run the tools cited above? Do they typically page to disk if memory is not available or just fall over?

On the data storage side, I think we would be ok to start with as there will be a dedicated SAN of 24TB with spare bays.

Finally, we would like to use VMWare and use the server as a host (but just for one virtual server). Would this present any issues?

Thank you for any advice that can be provided.


If you have some thoughts, please post them over there. Or if you are curious about what kind of infrastructure this work takes, go have a look.