System for Highthroughput Bioinformatics Usage

Forum Systems : New Build System for Highthroughput Bioinformatics Usage

I cannot afford the $20,000 some of these companies want for a bioinformatics ready machine, so I'm attempting to build one. I'm trying to stay under $1500, but I am also trying to use quality parts. I need high read/write speeds and high RAM, because I am dealing with whole genome mapping which is basically a brute force algorithm that maps patient data against the human genome in order to find mutation sites. I have never built a computer before, so please, please forgive me if I've made a totally noobish error. As of right now on my current machine, its taking me 11 hours to map a single patient against the human genome. I'd like to get that time down to under 4 hours if I can.

Power Supply: Corsair Enthusiast Series 750-Watt 80 Plus Bronze Corsair Enthusiast Series 750-Watt 80 Plus Bronze

Motherboard: ASUS Socket 1366/Intel X58/Quad SLI & Quad CrossFireX/SATA3.0&USB3.0/A&GbE/ATX Motherboard s SABERTOOTH X58

Processor: Intel Core i7-960 Processor 3.20 GHz 8 MB Cache Socket LGA1366

Primary SSD: OCZ 120 GB Vertex 3 SATA III 6.0 Gb-s 2.5-Inch Solid State Drive VTX3-25SAT3-120G

Secondary HDD: Seagate Barracuda Green 2TB SATA 6Gb/s 64MB Cache 3.5-Inch Internal Bare Drive ST2000DL003

RAM: Kingston HyperX 24GB Kit (6x4GB Modules) 1600MHz DDR3 DIMM Desktop Memory (KHX1600C9D3K3/12GX)

Graphics Card: GeForce 520

I also need to know what extra cooling methods I need to take. I am going to be using a corsair case which retails for something like $40. It only has two fans built in, so I'll probably need to install a few more.

Reply to SovereignThinker

^ Which Corsair case are you talking about ?? Also if hitting $1500 top limit is fine, then you can get the 6-Core i7 for that build,...
i7 970
http://www.amazon.com/Intel-i7-970 [...] B003UATLOS

ASUS Sabertooth X58 + Mushkin 12GB DDR3
http://www.newegg.com/Product/Comb [...] mbo.667759

Mushkin 12GB kit
http://www.newegg.com/Product/Prod [...] 6820226192

OCZ Agility 3 120GB
http://www.newegg.com/Product/Prod [...] 6820227726

Corsair 650TX + Samsung F4 2TB
http://www.newegg.com/Product/Comb [...] mbo.668391
This 650W is as good for your needs,...

GT430 - More powerful than the 520
http://www.newegg.com/Product/Prod [...] 6814130580

Total without case - ~$1457 | 1367 After rebates,...

Reply to gkay09

Wow, thanks. I didn't realize newegg had bundles, which really offers a savings for superior equipment. The mushkin ram cards seem to be out of stock right now, but otherwise, that seems very dooable. I really like the ssd, didn't realize there was a better one available for the same price range. I'd love to go up to the 6 core, but that price just stings. I guess its one of those things I'll just have to view as a more long term investment.

Cooler Master SGC-2000-KKN1-GP Storm Scout ATX/MATX/ITX Mid Tower Case (Black)

They seem to have this regularly for around $40 on amazon... even then the regular amazon price is only $60, so it may be a good option.

Reply to SovereignThinker

you should really be considering a sandy bridge processor such as the i7-2600K. nice comparison:
http://www.anandtech.com/bench/Product/287?vs=100

------------------------------ HIGHEST OVERCLOCK RECORDED (9GHZ):
http://bit.ly/SvyUi
"Well, there may be a reason why they call them 'Mac' trucks! Windows machines will not be trucks."-MS CEO S. Ballmer
My Rig
Reply to ps3hacker12

You should also check into if the brute force things you are refering to have been optimized for CUDA or OpenCL because with a 580GTX you could be looking at reducing the time from 11 hours to minutes if there is CUDA optimization. 6 core 12 thread CPU vs 512 CUDA cores the CUDA cores win

The idea is the same as the in the folding at home stuff I gather, and the video cards are massively faster at handling these than CPU's.

Reply to rvilkman

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System for Highthroughput Bioinformatics Usage

Forum Systems : New Build System for Highthroughput Bioinformatics Usage

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