This is the first post in a series where students will have the chance to write about their favourite tech tools to get the job done. This includes software, hardware, mobile apps, etc.
I am an experimental petrologist, high temperature geochemist and a general geologist. This is what I use.
Nothing too exciting here: I use Microsoft Word. I tried exploring the world of LaTeX (directly and using LyX), but it failed miserably. Not because I didn’t know how to use it, but because no one else is using it. I even wrote my entire MSc thesis in LaTeX, and it’s beautiful. The problem is that everyone else in the geochemical community uses Word. Most journals only accept Word format files, and those that take LaTeX convert it to their own format during typesetting anyway, introducing errors. So why bother? The latest versions of Word (2013 and above) are actually pretty good. Most bugs are gone, it’s capable of doing referencing, cross-referencing, document structure, etc. I don’t see a reason not to use it.
For text files I use Notepad++, which is an excellent substitute for Windows Notepad.
I don’t like printed paper. It’s a physical object that you have to carry around, it takes space, and it can get lost. With a toddler at home, it can also get eaten, torn apart, or destroyed in all kinds of enigmatic ways. Instead, I use Mendeley, a really good reference manager. You can load all of your PDFs in there, and it saves them in the cloud. At the moment I have 667 documents in my library, and I didn’t even use all of the available free space they give you. It has a PC desktop app, mobile apps (for Apple and Android) making your files accessible from anywhere. This is extremely useful. You’re on the SEM or the EPMA and want to see something you just remembered that was in some paper? There. You’re at a place without a mobile device? You can also access everything from their website. Easy. You can easily annotate and comment on papers, and it syncs it to all of your devices.
It also has a good Word plugin that automatically formats the references. It has a preset for just about any journal worth submitting to, and it usually works really well. It has some minor nuisances though, not everything is perfect. Still better than doing it manually, or figuring out why things like JabRef don’t work like they should.
I tried them all: Google Drive, Apple iCloud, Microsoft OneDrive (theirs and the one provided by ANU). The only one that I am happy with is Dropbox. It’s fast and reacts almost immediately to any changes in the files. It syncs very effectively, with files immediately updated across all of my devices (4 PCs and a mobile phone). It works so efficiently I actually do all of my work in the Dropbox folder itself and don’t use it as backup. I upgraded to Dropbox Plus, which gives me 1 TB (I don’t even have that much in my entire hard drive!), of which I’m currently using about 60 GB. This includes all of my MSc and PhD data and a bunch of other stuff.
The best feature of Dropbox is the ability to restore old versions of files. Have you accidentally overwritten something very important? No worries! Just go to the website and get the old version. This was a life saver on several occasions already. As far as I know, it remembers 30 days and it can be expanded to one year if you pay them.
I used to have those USB drives you get for free at conferences, but I got tired of how excruciatingly slow they were. Copying 100 MB of data would take many more minutes than it should! I have better things to do with my life. I bought myself a SanDisk Extreme USB drive, and this thing is fast. When connected to a USB 3.0 port (the blue one), it copies in seconds. Anything under 200 MB is copied fast enough that you don’t even get to see a progress bar. Of course, things like this tend to get lost so I attached a TMNT keychain to it, just in case.
Data analysis and plotting
I’m a huge fan of R. It’s a programming language originally developed for statistical analysis, but has since been expanded to do just about anything. It’s free and open, you can install it on whatever you want. Yes – even on your phone. It has hundreds of packages that expand its capabilities, which is what we lazy scientists want. If someone else did it, why do it again? Some of these packages are designed by and for geoscientists as well. One of the best parts of R is the plotting capability. It can plot just about anything you want, quickly and easily. The use of an IDE such as RStudio makes everything even easier.
It has two major drawbacks in my opinion:
- It’s rather slow. Other languages, such as Python or Julia, are much faster. But the ease of use more than makes up for it, and we geochemists rarely use data sets large enough to justify moving to something else.
- It’s a programming language. You will need to know how to program. There are no point-and-click things in it and you will spend time trying to understand what’s wrong with your syntax and why stuff doesn’t do what it should do. It is, however, easier than Python, MATLAB and the likes (in my opinion). And whenever you don’t know how to do something, just Google it. Someone else had the same problem before you, and was answered somewhere on the Internets (probably Stack Overflow).
There are two major reasons to use it (or any other programming language):
- It saves time. If you can teach a computer to do something, why not do it? Do you prefer point and clicking, copying and pasting, moving between spreadsheets, getting lost, or writing some code and running it?
The above figure sums it up (source, but also see this xkcd).
- It makes your science reproducible. You have your input files (txt, csv, xlsx, whatever), you press a button, and it gives you a publication-ready (almost) plot. Something changes in your input file? Have more data? Just run the script again. It’s self documenting. When using Excel, often you would have to click stuff and copy-paste some other stuff to get from your input to your output. It’s very hard to document that, and it renders your research unreproducible—by you, or by anyone else who might want to do it (your supervisor, the student that will come after you, or the person who downloads your data from the supplementary files in the paper).
That said, I do use Excel occasionally. I find the Solver feature extremely easy and useful (and then import the xlsx to R), and sometimes you just need to see a spreadsheet in front of your eyes.
It’s important to use vector graphics software when making scientific figures. Got a line drawing, a graph, or even text on a photograph? You need vector graphics. These files are editable and the end result is superior in quality. I used to use Inkscape for a long time, because it’s free, extremely easy to use and it was perfect for my needs. I recommend anyone who has no experience with vector graphics to give it a try. However, it’s also very slow and buggy, so I ended up buying CorelDRAW Home & Student Suite which is heaps better than Inkscape. Although not perfect, it clearly demonstrates the difference between a community developed open source software and one developed by professional people getting paid to do it. While many people prefer Adobe Illustrator (and it is the industry standard), CorelDRAW H&S is so much cheaper and I have yet to find a feature that I needed missing.
For raster image editing and manipulation, I use Paint.NET for quick and dirty work, and Corel PHOTO-PAINT (comes together with CorelDRAW) for more serious stuff. Again, Adobe Photoshop is most people’s favourite and the industry standard, but PHOTO-PAINT works just fine and I am happy with it.
If there’s something that I hate more than paper, is writing on it. My handwriting looks terrible, and it’s not because English is not my native language. It looks awful when writing Hebrew as well. I finished 5 years of university (BSc+MSc) and I used only about one notebook for everything. In the 4 years since I didn’t finish a second notebook yet. That’s because I use OneNote instead. As with Mendeley and Dropbox, it syncs automatically between all devices, making my notes easily accessible on my mobile phone and elsewhere. I must admit that I didn’t try any other alternatives too much. I used Evernote for a bit, but came back to OneNote.
Probably the most important productivity tool: music! As a huge fan of all styles and sub-genres of electronic music, I spend most of my days listening to Digitally Imported (di.fm), the most perfect online radio station ever created on this planet. As usual, it has a mobile app so you can listen on your phone as well. After signing up to their premium service, I found out they have a sister station called RadioTunes, which has non-electronic (well mostly) music categorised to a billion different genres, from Taylor Swift and Justin Bieber, through Reggae to 60s rock and more. Highly recommended!