Question

Computer specs for Bioinformatics

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6.4 years ago

NB ▴ 960

Just looking for recommendations to buy a Desktop for a Bioinformatician. The budget is £1000 (preferably less :-( ) We already have a powerful HPC on which we run NGS analysis/store fastq files.

This computer would be to run small applications and test scripts and store a bit of data, if needed. Currently I am looking at the following computer

DELL OptiPlex 7450 All-in-One

Processor: 7th Gen Intel® Core™ i7-7700 (QC/8MB/8T/3.6GHz/65W); supports Linux

Memory :8GB (1x8GB) 2400MHz DDR4 Non-ECC

Hard disk: 2.5inch 256GB SATA Class 20 Solid State Drive

Is there anything else I should look for, for example RAID or increase the memory to 16-24GB or include an external HDD ?

Many thanks,

computer specs desktop • 5.7k views

ADD COMMENT • link updated 6.4 years ago by Devon Ryan 104k • written 6.4 years ago by NB ▴ 960

score 3 · Accepted Answer · 2017-12-11

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6.4 years ago

Devon Ryan 104k

A bit more RAM never hurts, but if you just need this for small apps and test scripts then what you've already listed should suffice (for reference, my desktop has a similar use and it's a Dell Optiplex 9020).

If you normally process files on a cluster then I assume you can get access to that file system from your desktop too. Then there's little reason for additional storage.

ADD COMMENT • link 6.4 years ago by Devon Ryan 104k

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Thanks Devon and is having RAID 0 or 1 of any use ?

ADD REPLY • link 6.4 years ago by NB ▴ 960

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I definitely would add more RAM, so make that at least 16GB. You should also have additional Storage besides SSD (but as Devon mentioned, that could also be somewhere else. And this network storage most likely is backed up (?) regularly, then you would not have to do that on your machine again - assuming you save your stuff regularly to that file system)

ADD REPLY • link 6.4 years ago by LLTommy ★ 1.2k

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Nans : Not particularly. SSD's are rated for a particular number of reads writes. If you write a large amount of data to local SSD's you will wear them out quickly. 256G is not much space for analyzing NGS datasets locally.

Get a single SSD as a system drive and then a couple of TB of spinning disk for your local bulk storage. As others have said, getting 16G RAM is first order of priority. Having two sticks of RAM will allow your system to use the dual channel memory which will provide nice speed boost. If you can only get 8GB then go with 2x4G for the same reason.

ADD REPLY • link 6.4 years ago by GenoMax 141k

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Thanks genomax. We are not going to be analyzing or running NGS data on the computer. We have a huge cluster for that. This is just a desktop for minimum bioinformatics work/writing scripts/using IGV viewer and running small applications. As you can see, we are on a very tight budge of £1000 so not sure we can can afford a couple of TB. Maybe 256 SSD + 500Gb HDD configured on RAID 0 or 1 ? Increasing the RAM to 16 (2x8Gb) is a good idea.

ADD REPLY • link 6.4 years ago by NB ▴ 960

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Have you considered dropping that i7 to a i5? If little work is going to be done locally then having an i7 CPU is overkill. That should free up money for a bigger local disk. If you do want to use RAID of any kind then use identical disks.

ADD REPLY • link 6.4 years ago by GenoMax 141k

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Even medium sized RStudio and IGV sessions will soon exhaust 8GB of RAM. I wouldn't really want to run a office PC with 8GB these days. It cast less than £100 to go to 16GB. I'd definitely go for an i5 with 16GB of ram and 128GB SSD + 1TB HDD over the config above.

ADD REPLY • link 6.4 years ago by i.sudbery 19k

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At least in our case anything important is on a separate (backed up!) storage array that's also used (in part) by the cluster. Then there's no reason to bother with RAID.