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Old 03-24-2011, 11:22 AM   #1
Giles
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Location: Birmingham, Al

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Default Which System to use? PC vs Mac

I'm crossing the threshold of NGS from total newbie to bona-fide intermediate. I've been using Galaxy and am beginning to reach the point where I need to write my own code and to use the available codes to do some of the more difficult computation. I realize that having a windows machine is useless. So, my question is, should I get a new PC and install a Linux based OS..or should I get a MAC running OSX?
If you say Linux, any advice on which version is best for a newbie; and where is the best place to order a PC w/ multiple processors?

Basically, any information for setting up a nice computer to do NGS analysis is very much appreciated.
Thanks, Keith.
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Old 03-24-2011, 01:41 PM   #2
ssnowfox
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Quote:
Originally Posted by Giles View Post
I'm crossing the threshold of NGS from total newbie to bona-fide intermediate. I've been using Galaxy and am beginning to reach the point where I need to write my own code and to use the available codes to do some of the more difficult computation. I realize that having a windows machine is useless. So, my question is, should I get a new PC and install a Linux based OS..or should I get a MAC running OSX?
If you say Linux, any advice on which version is best for a newbie; and where is the best place to order a PC w/ multiple processors?

Basically, any information for setting up a nice computer to do NGS analysis is very much appreciated.
Thanks, Keith.
I suppose ubuntu may be the best choice for you. for its operation is much easier, and workstation is preferred. you can search deals through google, good luck
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Old 03-24-2011, 02:08 PM   #3
fpepin
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I'd say whatever makes you most comfortable. I'm fond of OS X as a desktop machine because I can also use MS office & Adobe illustrator and such. The Mac Pros that you'd want to do serious analysis are pretty overpriced, unfortunately.

The advantage of linux is that it's cheaper (hardware more than software) and compiling code can be easier there than on OS X. Generally both will work nicely when building code, but you can get incompatibilities on OS X every once in a while.

Ubuntu is indeed a decent choice if you want to go linux. If you have an administrator that will be taking care of things for you, feel free to go with what he/she recommends, especially if you won't be using the machine graphically. Many of the distributions have Live CDs, so you can also try a few before installing.

As for where to buy, you can either ask your local computing group (if any) or just go with Dell. They're generally reasonably priced and you'll get something reliable without having to worry too much about it. If you go with Apple, your options are obviously limited, although you can save a pretty penny by buying the RAM separately.
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Old 03-25-2011, 07:30 AM   #4
schmima
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hm - the apple computers (Mac Pro) are definitely overpriced... The basic configurations seem to me a bit useless for NGS data - the cheapest one (2900 CHFr) ships with an Intel Xeon, 3GB RAM and an ATI Radeon HD 5770... -> not enough RAM and a graphical overkill (as long as you don't want to calculate on the GPU). For only 2000 CHFr you'll get an Intel i7, 24 GB RAM, WD VelociRaptor (600 GB) & a cheap harddrive with 2 TB and a very cheap graphic card. In case you need a good graphic card, you add 300 CHFr more and there you go. Hence - assembling the computer yourself will save a lot of money. And well - if you really want to have the apple OS on it:

http://www.hackintosh.com/
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Old 03-27-2011, 06:13 PM   #5
n00c
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Actually Linux would be first choice because quite a few NGS bioinformatics tools are compiled with Linux in mind (to work on clusters, etc.).

A Mac is nice as a secondary workstation or as a laptop, but I would definitely want to have at least one Linux server/workstation around. Mac Pro is on the expensive side (especially when compared to building your own system), but it is extremely nice hardware, and you can run Linux on it as well (doesn't have to be Mac OS X).

I would not go the Hackintosh route... Either set up a Linux box or get a real Mac.

Last edited by n00c; 03-29-2011 at 05:34 PM.
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Old 03-27-2011, 08:28 PM   #6
Kennels
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I would also recommend Ubuntu Linux as it is free, support and information of NGS software and such on this platform is abundant, and installing it is pretty simple. You can find the latest version on its website with step by step instructions on how to install.
I actually have a dual boot system with windows 7 and Linux (use the 'Grub' software to manage the booting up - alot of info about this by googling), though I hardly use Windows - it's just there for the occasional need to use MS office. Ubuntu has the 'OpenOffice' applications that are parallel to Word, excel and powerpoint, though from experience performance isn't as good as MS when the file gets really big.

Beware though of alot of 'Gotchas' when using linux - installing flash or Java, browser plugins and even adobe pdf require some workarounds, but you usually get workaround info after surfing around the net for 5 hours if you're a newbie like me

I built the computer from scratch with 6 CPU cores (AMD phenom) and only 4Gb RAM on a Gigabyte motherboard (it is much cheaper to build from scratch if you're up for it - again lots of resources about this on the web), but you'll find that alot of the software out there are still not designed for parallelization so you'll still be using maybe only 1 or 2 CPUs for any given analysis (actually take that with a grain of salt as some commonly used programs (e.g. bowtie) does have parallelization of CPUs). However, getting as much RAM as possible would definitely benefit you down the road. Also, get as much hard drive space as possible. If you install windows too, give maybe 40 to 60Gb to it and the rest to linux. A well known maker of hard drives is recommended (e.g. seagate) as i've had experience with relatively new HDDs dying with my data on it....
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