Source
r/bioinformatics•
jayphive

Help with choosing a computer

technical question

I am interested in purchasing a new computer to do some bioinformatics on, for my home use. We have a bioinformatics computer at the lab that works well with 64 gig RAM. We do a lot of RNA seq analysis on infected plant tissues to identify viruses in these samples. We also do some de novo assembly of viral genomes from these samples. I’d like to buy a new 27 in iMac, but curious what other people think about what kind of computer would be best along with some recommended tech specs.

Posted May 3, 2021, 5:31 PM UTC

2420
RevolutionaryPin6014•

Buy something like a Dell Optiplex 7070 and then add in 64Gb of RAM to it and install Ubuntu / some other Linux distribution on it. Macs are great but not good value for money for this kind of thing.

35
Starcaller17•

I recommend just building your own with the exact specs you want and putting Linux on it. Far cheaper and easier to upgrade than anything made by apple.

20
vinayjrao•

There are two options, 1. buy/build a computer with good to great configurationsrunning Linux, or 2. buy/build yourself a computer with decent configuration running Windows/Linux/OS X as per your convenience, and connect to the computer in your lab, or any other institutional server you might have access to. I would recommend going for the second option since you don't put too much load on your PC (I have burned my HDD while trying to analyze some RNA-Seq data on my previous laptop with 4 GB RAM. I have a laptop with 8 GB RAM currently, which I would put under the second category)

Edit: Even if your budget is considerably high, I would suggest you go for the second option, because if the computer ever breaks, you won't have to spend on having it repaired

13
Twelve_MonkeyssBSc | Industry•

If you have a remote computer for the heavy calculations, your base computer doesn’t have to be that heavy. I don’t really recommend something special, but I can share my Setup:

DELL Optiplex 9020 i7-4790 32 GB RAM 2x 500 GB SSD (one for windows and one for Ubuntu) 1x 1TB HDD nVidea GeForce GTX 1050 Ti

I personally also really enjoy working on two screen and therefore have a setup of two 25“ WQHD (2560x1440) monitors.

And a 2015 Dell XPS 13. More than enough power for some coding and the usual stuff.

11
Here0s0Johnny•

For linux, I'd buy an AMD GPU because of better open driver policies wayland compatibility.

3
Twelve_MonkeyssBSc | Industry•

You’re right…but I haven’t had any problems with the 1050 ti.

2
corkbar•

but what would you even use an AMD GPU for in Bioinformatics? last I checked, OpenCL was basically dead and machine learning, the only thing I'm aware of making heavy use of GPUs, was all CUDA and Nvidia based

1
Here0s0Johnny•

True. AMD for a snappy desktop and Nvidia for cuda.

1
MGNute•

If you're looking for something to do bioinformatics work on, a consumer desktop is not going to be an awesome choice. It has to do mainly with the way the memory bandwidth is set up, but if you look at the STREAM benchmark on consumer hardware like the intel i7 or something like that, you'll find that the bandwidth does not scale well with the number of processors used. The reason is that it's not really designed to, but in bioinformatics that memory bandwidth often pretty closely correlates with the effective speed of the jobs that you're going to run. Something like an Intel Xeon is designed differently in that regard, and you'll actually see good speedups as you run things with mutliple threads/cores. As I understand it the AMD chips these days are outpacing the Xeons, but I haven't actually tested any of those so I'm not familiar which ones are good. But I think this is why the others here have recommended either building your own or buying something in the workstation class. I built one myself last year and would be happy to share the specs on that if your'e interested.

7
jayphiveOP•

I’d love to hear the specs thanks

3
Rowhan-•

I was once like you and assumed that it made sense to run things locally or on a lab cluster, but then I tried working on cloud, in particularly https://www.digitalocean.com/.

Working on cloud is so awesome and incredibly cheap as you will usually only need 24h up time per week if you got your pipeline properly prepared.

I would therefore simply buy a nice MacbookPro and do all the heavy lifting on cloud machines. Nothing like spinning up a 256GB memory machine and chewing through a RNA-seq dataset like a hot knife through butter

7
Aquanker•

This is the right comment here. Choose your tool that you like and outsource computation to cloud. Everyone else in this thread ignored the fact that you may prefer mac over pc. I work for a bioinformatics company and everyone has the choice of Mac or pc and the co founders all use macs.

3
gottapitydatfool•

Second this. Any heavy processing should be done on the cloud. Your concerns should be the following:

  • Screen real estate
  • Good keyboard
  • Maybe battery
2
jayphiveOP•

To expand on my original post.... I currently have a very old 27in iMac, which doubles as my TV. I like the large screen for writing manuscripts/editing figures/bioinformatics. I dont want to rely on the lab computer at all, due to access issues from COVID, and to leave that computer for my students.

I really dont know computers, and dont have the time to learn. I’m willing to spend a bit more for familiarity and convenience. Thank you all for your great replies

3
throwitaway488•

Honestly you are probably better off just connecting to your lab computer or another cluster remotely using SSH. All your data will be in one place, and the machine is optimized for those large computations. If you really need to do the analyses on your home machine (ie your lab one is always 100% utilized) then building a machine to your own specifications and running linux is probably better.

3
luxii32•

I would be against an iMac. Buy or Build a Desktop yourself. You can then upgrade parts if it is necessary, which is not possible/hard with Apple devices.

I am curious why you "only" need 64 GB of RAM for calculations. Sometimes I use more than 200 GB (and I could easily consume more) and prefer to connect remotely to my server which has the needed resources.

2
WhatTheBlazesPhD | Academia•

Get a dell or apple laptop of your choice. Nothing excessive but don't limit yourself, overall specs mostly irrelevant in my experience. For home use a secondary monitor is a good investment too.

2
k-atwork•

My work is primarily on an AWS instance. Mainly so that I can bump resources easily. The computer itself is an old 2015 mac book pro. As long as it runs chrome/vim/intelliJ I'm happy.

1
thriftyplantmomma•

If you get something with Windows 10 Home, weird things happen when you try to install things. I'm the only one in my PhD cohort who seems like my computer misbehaves. I have a Huawei by the way

1
corkbar•

You should seriously consider just connecting to cloud instances like AWS, GCP, etc., and doing the work there, instead of buying your own hardware. For short-term or small scale projects, you will likely save a lot of money. For large or heavy projects, you will need to do the math and estimate your needs and costs before investing in your own hardware.

If you really want to have your own hardware, I would not get an iMac. They are wonderful to use at work and home to connect to the remote Linux server for data analysis, but they are pretty expensive and practically impossible to upgrade, and simply not designed for constant heavy workloads.

A good start if you wanted to build your own would be something like Ryzen 3950X (16 cores / 32 thread) with 64-128GB RAM, and as much SSD space as you can get. You do not want to try and do heavy bioinformatics work off of consumer HDD's, they are terribly slow unless you rig them up in some kind of faster RAID array (at which point you might as well have just bought SSD's and done the same instead for even better performance).

1