Question: Which laptop will be good for most common and advanced bioinformatics works?
1
gravatar for ThulasiS
2.4 years ago by
ThulasiS60
ThulasiS60 wrote:

Hi All

I need some advices and suggestions in choosing a machine for regular bioinformatics and some advanced modeling works and mostly deal with sequence and data analysis. I am in dilemma in choosing model and select configuration. Which one will be better A laptop with 8gb ram and 128gb SSD or A laptop with 16gb ram and 500gb HDD. I heard SSD is better option even though it is bit costly. What will you suggest. In my mind I am thinking of buying Apple Macbook air with 8gb ram n 128gb SSD.

Please give me some suggestions

Thank you

suggestion • 4.1k views
ADD COMMENTlink modified 2.4 years ago by Joe16k • written 2.4 years ago by ThulasiS60

Think about the criteria that are important to you: - What kind of tasks will you run on it ? I/O-heavy operations require fast disk access. For example, database requests are ~10-100x faster with an SSD than with a 7200 rpm disk commonly found in laptops. More memory will offer more caching that could offset the slow disk speed. Memory usage depends on the size and type of the data you want to process, how you process it and what other tasks are running simultaneously. For example, a 20000 x 20000 numeric matrix occupies 3.2 GB in R and a 1 million rows x 100 columns numeric data frame occupies 800 MB. - What operating system should it have ? Many bioinformatics software run on Linux and using Linux might facilitate interoperability with your compute farm if you have access to one.

ADD REPLYlink written 2.4 years ago by Jean-Karim Heriche21k
7
gravatar for i.sudbery
2.4 years ago by
i.sudbery6.9k
Sheffield, UK
i.sudbery6.9k wrote:

It really depends on why you are buying a laptop. Firstly if what you need is a computer, not specifically a laptop, then buy a desktop. A desktop with 32GB of RAM and a 4C/8T Xeon CPU will probably be cheaper than any laptop you could buy that could do bioinformatics. On the other hand, if you do need to be mobile, ask: how much actual computing do I need to do on it, or will it mostly be a dumb terminal connecting to cloud or HPC compute resources? Several companies can provide you with a powerful linux box in the cloud for free, or a small per hour cost. We do almost all our work on the universities HPC cluster, so our own computers most just act as screens and keyboards for that. In which case, choose the machine with the nicest screen and keyboard!

There is a limit to how much sequence analysis you can do on any laptop, and generally the limitation is going to be RAM. For example, the STAR RNA-seq mapper requires at least 24GB to map to the human genome (other, more memory efficient, mappers are available). Also datasets can be large - 100GB for a sequencing dataset would not be unusual. Look at it this way: faster CPUs and SSDs will help you get work done faster, but they won't change what you have the ability to do. More RAM and more disk space will allow you to do things you won't otherwise be able to do at all.

With that in mind, if I wanted to buy a laptop to do bioinformatics on, i'd look for something with at least 16GB of RAM and at least 500GB disk. If I had extra money, I'd use it to go to 1TB or even 2TB spinning disk, and 24/32GB RAM rather than getting an SSD (however much nicer SSD makes life). I would not get a MacBook Air. If you can't afford MacBook Pro, don't get Apple.

ADD COMMENTlink written 2.4 years ago by i.sudbery6.9k
0
gravatar for bharathramh
2.4 years ago by
bharathramh30
bharathramh30 wrote:

getting apple with 8 GB Ram is almost equivalent to a 16 Gb ram normal laptop. But at the same time Apple is not advisable for Such Bioinformatics works, Buy 16 GB RAM normal laptop With Ubuntu/Any Linux . And be Virus Free :P

ADD COMMENTlink written 2.4 years ago by bharathramh30
1

apple with 8 GB Ram is almost equivalent to a 16 Gb ram normal laptop

Eh? Not convinced by that. I know this is anecdotal, but in my experience, Apple is even worse for background processes. Sat in front of my mac and Win 10 PC right now, both with only Chrome running, an equivalent number of tabs, and both with 16GB RAM, my Mac is running at 9/16GB used, and my PC is at 5/16GB. Both my machines are basically idling, and the Mac still has over 100 more processes running in the background (just system ones! Not even apps I'm running myself!). If anything, my PC has more user processes running in the background too as it's a media/Plex/remote desktop server.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Joe16k

OS X just manages resources better when we have a LOT of processes running. Plus the UNIX file system is super helpful. The seamlessness of hardware components structuring means that the machine as a unit is better than Windows, which is a bunch of parts from different companies talking to each other. I'd get Apple just for their backup capabilities and memory management when on low memory.

ADD REPLYlink written 2.4 years ago by RamRS25k

In the end, MacBooks are also bunch of parts from different companies talking to each other. In my previous job, I had a maxed out 15" MBP and at home I have a maxed out MBA. However, I'm not going to buy another MacBook ever again, the main reason being that I don't like where macOS is going. It would not surprise me at all if a few releases from now they allowed you to install stuff from nowhere else than the AppStore. I also wouldn't be too surprised if they ditched Intel for their own CPUs relatively soon, i.e no more x86 and bye bye all bioinfo software. Also, macOS is no replacement for Linux and manufacturers have really stepped up their game as you can now buy machines with Linux preinstalled and everything. Windows 10 with Windows Subsystem for Linux isn't that bad either. And that touchbar thing, making the keyboard worse.. just why? Don't get me wrong, I'd happily switch my Dell Latitude 7280 for a MBP (one without the touchbar).. however, if I had Dell XPS DE.. no way would I downgrade to a MBP.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by 5heikki8.6k

Yeah I agree with both of the above - Time Machine is fantastic. In fact, I've always liked Apple for their hardware, but not their software generally. Having a MBP which used to have a 9 or so hour battery life when it was new, the magnetic chargers, aluminium unibody, and hands-down the nicest trackpad/gesture support in the world is something I would sorely miss if I moved back to a different device (not that Apple has a monopoly on many of those things any more).

When Apple decided to lock down the permissions of loads of system paths in the latest OSs it caused me endless hassle.

That said, I wouldn't go anywhere near the newest iteration Macbooks. The new ultrashallow keyboards are horrible. Mine is a 13" mid 2012, and the last model I'd consider having is their 2015 ones which are basically the same.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Joe16k

I use the 2016 MBP with TouchBar. Zero complaints, although I do prefer my older MBP. It's not Windows I hate the most, it's the PC manufacturers - Dell, Toshiba, HP, etc.

ADD REPLYlink written 2.4 years ago by RamRS25k

Oh okay.. I understood thank you

ADD REPLYlink written 2.4 years ago by ThulasiS60
1

linux.... all the way.

ADD REPLYlink written 2.4 years ago by YaGalbi1.5k
0
gravatar for ThulasiS
2.4 years ago by
ThulasiS60
ThulasiS60 wrote:

Hi

Now a days mostly all the laptops per-installed with windows and an average laptop with > 12gb ram costing more than Indian rupees 70k. Too costly I am rethinking now

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by ThulasiS60

Where are you looking to buy these laptops for 70k?

I bought my laptop 3 years ago n London for £550GBP. It has 16GB RAM, 4 CPU cores, 1TB hard-disk, and there's a graphics card somewhere inside too. I wiped Windows off it straightaway and installed Ubuntu 14.04.

I do a lot of work on it and it's really great for general bioinformatics. For more heavy tasks like whole genome, I just use 'the cloud'.

For the record: Windows has lots of very useful programs and the best set-up for me is both a Windows and Linux machine (one accessing the other via remote desktop within an internal network).

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Kevin Blighe54k
1

Sorry 70k in Indian currency and still 550GBP is cheap..thank you

ADD REPLYlink written 2.4 years ago by ThulasiS60
0
gravatar for ofonov
2.4 years ago by
ofonov10
ofonov10 wrote:

Well, it really depends on the tasks you work with. Most of computationally intensive work is done on servers/clouds, with at least 64 Gb RAM and TBs of storage. E.g varinat calling pipeline on WGS can require 128 Gb of RAM, 16 cores and 5 TB of storage, while processing the data. On laptops some smaller tasks can be done, but again, depends on the tasks. If you do need a laptop which can be used for bioinformatics, a good price/performance ratio can be achieved with a Linux based system, however Apple OSX offers significant convenience for everyday tasks. If you do not need to carry around your machine, you can get a better price/performance ratio by getting a tower(desktop).

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by ofonov10
0
gravatar for 5heikki
2.4 years ago by
5heikki8.6k
Finland
5heikki8.6k wrote:

It really depends what you're going to use it for. At work I get by with Dell Latitude 7280, but I really only use it for making a remote connection to one of my towers (one has 32 cores, 128GB RAM, 512GB SSD and 2TB Raid array, another 48 cores, 256GB RAM, 1TB NVMe SSD, 8TB Raid array) or compute clusters (with some nodes having up to terabytes of RAM). If I could choose any laptop, I would go for a maxed out Dell XPS DE 13 or 15.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by 5heikki8.6k
0
gravatar for Joe
2.4 years ago by
Joe16k
United Kingdom
Joe16k wrote:

For bioinfx, I'd suggest Linux in general. Most standard laptops will be fine for bioinformatics tasks. There isn't often a line between suddenly being able to run a program and not (unless that difference is 8 extra GB of RAM for example). Chances are the types of work that are out of reach for a $600 laptop, are also out of reach for a $1000 laptop. You'd almost certainly need access to cloud or dedicated server computing.

I personally use a Mac that's now 5 years old, I've stuck a bit more RAM in it (now at 16) and a solid state drive (it's the best thing you can do to improve the day to day feel and experience of handling the machine). I do very little computation actually on the machine though.

I usually despise apple products. I use this mac because it was given to me via my University. I've learnt one thing since having it that I like though. Having terminal as part of the OS is gold. OSX has the benefit of supporting a lot of mainstream software that Linux doesn't or didn't (e.g. the ACTUAL microsoft office suite), whilst also retaining a lot of what's good about UNIX-y systems. Also having the same filesystem (paths etc) as Linux is really useful. Copying files to and from a windows machine to a linux machine can be a real pain.

Via BOOTCAMP, I can also get access to the odd bit of software you find that's Windows only. Surprisingly frequent even now.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Joe16k

Copying files between Windows and Linux is very easy with Windows 10 since you have Windows Subsystem for Linux, i.e. you can use rsync/scp/whatever. I'm rather enjoying the default Ubuntu it comes with (16.04). In fact, 99% of my time on this laptop I'm just running "Ubuntu Bash" full screen with tmux. There are still some problems though, for example, you need a mouse for copy&paste. Workaround is to use Emacs for everything, there M-w and Ctrl-y work as they should ;)

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by 5heikki8.6k

TeamViewer, i.e., remote desktop, works pretty well too for file transfers. I'm not sure which protocol it uses though. I sometimes work across continents and frequently have to transfer files across the Atlantic!

ADD REPLYlink written 2.4 years ago by Kevin Blighe54k

That's true now, but wasn't always the case. There are still considerations when copying files between systems because you can run in to issues with the carriage return characters etc. It's also a subsystem, rather than being the OS 'itself' which is bound to come with tradeoffs.

ADD REPLYlink written 2.4 years ago by Joe16k
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