Digital Researcher Education

Building a Linux computer for imaging and informatics

Parts for a fast Linux computer
Parts for a fast Linux computer

I’m going to show my age here, but it is 30 years since I last built my own computer! What a change. The job then involved lots of razor sharp metal edges, drilling out dozens of holes, hundreds of soldered connections, not to say a particular memory of soldering up a 64-way ribbon cable only to have forgotten the cover, struggling with self-tapping screws that wouldn’t self-tap, bolts that were only too happy to self-tap, giant transformers with multiple undocumented taps of unexpected (high!) voltages, and a ‘correction’ list for the PCB (printed circuit board) involving cutting of a dozen of more tracks and addition of numerous lengthy jump wires. Then several happy days with an oscilloscope and probes finding PTH (plated-through holes) that weren’t, dry joints, adding power feed-wires because I’d replaced a few 74LS (low-power Schottky) bus drivers with 74S components … I don’t suppose many readers of this blog will remember those days.

Now, for £40/$60 you order up a case from Amazon and it comes with five fitted fans, as many screws as a Fastenal catalogue, turned edges, USB sockets and more. Equally, the £30 power supply comes with all the connectors and plugs for the £100 motherboard which has three video outputs, USB, wi-fi and the lot. I went for 32Gb of RAM: 1600 times the “huge” 20Mb hard-disc of my last home-built computer. Now it’s plug it together, snap in the processor which even comes with heat-sink compound on it, and power up. There were just a couple of glitches in not having one feeder to the motherboard (memories of the LS/S debacle) and an unexpected unplugged connection in a USB in the case. Then straight into the BIOS settings, and booting then installing Ubuntu Linux from a USB stick – the Linux I installed was Ubuntu 14.10 (now 15.04).

I suppose becoming familiar with Linux from the old PDP11 days with UNIX, and more recently the Android flavour on a tablet and phone has helped. But it really does work now! For basic usage, the change to Linux from Windows is certainly less than the change from Windows XP to Full-Screen 8 (the operating system known in marketing-speak as Windows 8 but only letting you run many programs in full screen). I’d played with a Linux OS only a relatively few years ago, and found it much less friendly than it is now.

A big need for me – like most botanists and microscopists, so being both means I am a double-user – is photo and video editing. Here, on the Linux box I have used two free programs, GIMP and ImageJ/NIH-Image and I like both of them – GIMP seems to do everything I would need from an image processor. However, after more than two decades of Photoshop, I know every function I need inside out: I’m five clicks from a Gaussian blur function to sharpen chromosome outlines in the DAPI channel of an image only. It is a long learning curve to reach that stage in GIMP – there are several options to download add-ins that make GIMP much more Photoshop-like, and I’m experimenting with these. However, with the huge cost of Adobe programmes now, I would really like to get up to speed with GIMP. For my botanical images, I have used Picasa as the indexing system on Windows; there are multiple non-identical equivalents for Linux.

Libreoffice is one of several free wordprocessing, spreadsheet and PowerPoint equivalents for the Linux system. I wouldn’t have been happy to change five years ago, but then everyone had to change anyway – the instability of Microsoft Word & co means I’m happy to learn yet another wordprocessor package. I do wonder about LaTeX? The Linux web-browers and some programs like Geneious that I use for bioinformatics are no more different under Linux than a ‘new-upgrade’ version on other OS-s (mostly the same but the odd annoying change). Of course, most free bioinformatics software runs on Linux, so that was a major plus in changing operating system.

For all the applications I use, the performance of the 32Gb i7 Linux machine is terrific! With my last few changes of computer, I’ve tended to upgrade them as they became full of bloat-ware and unreliable, rather than seeing any improvement in speed. Indeed, often the ‘latest’ operating system and program versions have been slower than their predecessors. Not so with the Linux box – it’s like getting a new computer in the 1990s!

So what did I build? I used an Asus Z97 motherboard (including graphics output to three simultaneous monitors, with wifi and wired internet included), 32Gb RAM 2440Mhz, an Intel i7 4790K processor, 256Gb SSD (solid state disk, to boot) and various hard disks. I put in a beefy power supply – it seems to me still that power supply capacities are overstated and motherboard/memory/disk power is understated, so I would order a PSU with at least double the apparent requirement. As I noted, I used Linux 14.10. I was originally planning to make it dual-boot with Windows, but I have not found a need for that.

We’ve been very lucky in botanical and cell biology fields that Japanese and Chinese characters, and then games, drove high-resolution graphics and fast processing – our needs – early. Unfortunately, the games hardware and tablet development has stopped computers going in the direction we botanists mostly wanted, now mostly making them for the consumption of media and taking the odd ok-but-hardly-publication-standard photograph. I can’t see these drivers changing soon, so hence the decision to build something faster. Maybe we researchers will need to do more hardware development again!

 

 

Edit 29/05/15: Made clear there are multiple free office/wordprocessing suites for Linux; added extra links.

2 comments

  1. Libreoffice is the wordprocessing, spreadsheet and PowerPoint equivalent for the Linux system. I wouldn’t have been happy to change five years ago, but then everyone had to change anyway – the instability of Microsoft Word & co means I’m happy to learn yet another wordprocessor package.

    Why learn a new when you can easily edit word docs, create and export them using the free online version of Microsoft Office for which there’s an add-on for Chrome which loads each application up in a regular window so it’s just like the real deal.. Google also lets you edit docx files.. Those who want an actual installed office suite on Linux which handles docx files should go for WPS office (Kingsoft Office).

  2. Thanks for comment – yes, the free online office programs work well, and I am a regular with Google docs.

    However, I am far from being ‘connected’ enough to rely on a web connection – whether during travels, in hotels which charge per device, or in the field. I did try the Chrome operating system on an Acer netbook and was very disappointed: it was not particularly fast, and couldn’t cope with intermittent internet. In my lab. they are more interested in checking your security details than providing a working system, so you needed to log-on again every 20 min or so (same at conferences where connections drop between sessions when everyone logs on).

    As I indicated, I find the difference between Excel 2003 (which I knew reasonably well) and Excel 2007 (minor changes only since then) was far greater than the difference between Excel and LibreOffice Calc. I’ve edited the text to indicate other Office software – I used WPS/Kingsoft on my tablet.

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