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The Freedom of Linux in Science

gconyersApr 17, 2018, 6:52:25 PM

When sitting down to write this post answering: why I chose linux as my daily driver, and how I use it, I really had to think. My first computer was a Commodore 64. I was enamoured with it.  I learnt how to programme with Basic. I remember creating something out of nothing, and being delighted when I could tweak the directions to make it something else. From there, I was hooked on using my computer fully, not just using it passively.

My journey through computer history:

My past computer use was as eclectic as you can imagine growing up in the 80s and 90s. As I grew up, the family shared a single machine. I don’t remember much about it except it was big, blocky, and it had the now cheesy AOL “You Have Mail!” alarm on it. At school there were all of three Linux machines - and they were in the library. Later, when I was in university, I had a selection of Windows, Macs, Sun, and few flavours of Linux machines. I used them all as necessary. Mostly because I could, and partly because it was convenient as I didn't have my own computer.

It wasn’t until I was in grad school that I chose to get my own computer that I wouldn’t have to share. Not only was everything mine to layout as I wanted, but I could control what programmes would go on it, how it was used, and possibly most importantly to me at the time, was a lack of grimy fingers on my keyboard. (Germaphobe here.)

Of all the machines I used, I fell in love with the OpenSUSE 7.0 I tried in a physics lab at my old college. So, naturally, OpenSUSE is where I gravitated to. The best part for a broke uni student was the price. Since then I’ve used 7.0 to the current version of OpenSUSE Leap 42.0 for all my science needs. I've not run into a single problem that I couldn't fix with a little creative coding (and often a lot of cursing at syntax errors).

OK, so how do I use it?

The thing that I’ve always loved about Linux is that no matter what flavour you use, it’s yours to do with as you will. You can use only native programmes, make programmes, or even use an emulator to use non-Linux stuff on your computer.

OpenSUSE is often used by administrators and network creators. It’s pretty simple to set up your basics, such as multiple drives, networks of computers and printers, and pretty much anything you can think of. YAST is intuitive to use, and the wizards walk you through most everything in case your brain is checked out. I’ve never had a problem with finding things that would “plug and play," which means I've had it easy for quite a while. And when I can't find it, I know I can make it with a bit of effort.

In my world of science, science communication, and as a business owner, I use my computer quite differently from what you’d expect from a Linux user. I don’t speak a lot of “computer-ese” as it were, nor do I programme a whole lot any more. (I used to when I had to build wrappers and the like to even get OpenSUSE to work with a router.) So, I’m going to break this section down into the areas I use OpenSUSE to give you an idea of how I use the various programmes. First personal since it’s the shortest list, then work.

Personal use:

Calibre ─ managing my e-books and reading every format under the sun

Tor Browser ─ because I can

Almanah Diary ─ to jot down notes and ideas

Tomboi Notes ─ virtual Post-its

VLC Media Player ─ to watch videos, duh

Clementine ─ music player

Discord ─ for socialising.

Work use:

Chrome ─ Useful for some things, need I say more?

Tor ─ Because it’s more useful than Chrome for privacy

Gnu Cash ─ Accounting and bookkeeping

LibreOffice ─ Writing, making presentations, nearly all of our handouts, database of inventory, etc.

Zotero ─ citation manager and tool

Audacious, AudioRecorder ─ record audio, edit audio

SimpleScreenRecorder ─ does what it says

PDF Chain ─ handy for manipulating PDFs and books

Gimp ─ image manipulation

Kdenlive ─ video manipulation

Scribus & Inkscape ─ make and manipulate vectors

View Your Mind ─ mindmapping

Zoom ─ conference calls and meetings

LibreCAD/BrisCAD/FreeCAD ─ designing things

Kalzium (with avogadro) ─ chemical data lookup, modelling, and manipulation

SciLab ─ number manipulation

SciPy ─ various science and maths manipulation

Bullet ─ for physics collision detection

ParaView ─ data visualisation

All this comes with a caveat: We are constantly exploring, learning what’s out there, breaking things, and fixing things at Insanitek. One week we might be using SciLab, another we might find a different tool that does what we want smoother. So far this is what I have on my computer, but there are several in the lab that use different flavours of Linux with different programmes that do similar things. They can all be opened on others computers, and that makes our lives so much easier.

If there is one thing we wish we had, but we don’t just yet, it is a specific scale that we can plug into the computer, then hit enter when the sample is weighed. I remember we had one at the soil erosion research center (SERC) at Purdue that did this. It made weighing out hundreds of samples much quicker. I’m still on the hunt for this mystical machine, and when I find it, I will get it. Even if it’s software is Windows-based, we’ll figure out a way to make it play nice with Linux. Because that’s what we do.

Others on Linux:

Eric Green

Mind's Gaming Community




Mark Edworthy (nearly all his blogs, seriously)