‘Tis the season of thesis writing! Well, in my office of fourth years (!) at least. By this stage of PhD life, most of us have our own ‘toolkit’ of computer applications that we’ve settled upon to complete the task, but in the first year or two, it’s a case of trying lots of options and finding the one that works best for your PhD and style of working.
Here, I’ve listed my top ten freely downloadable computer apps and accessible websites that have proved invaluable so far. I should mention that although I use a Mac, almost everything listed below has an equally useful Windows version (some entries are specific to petrology, so if you’re a non-geology PhD student, you can probably skip those bits…).
Click on the links below to go to each section
1) LaTeX
2) Detexify
3) Bibdesk
4) PDF to Word
5) R
6) Textwrangler
7) Tetlab/Trinity
8) Georoc database
9) Generic Mapping Tools (GMT)
10) MELTS
1) LaTeX
Writing a PhD is a bit like Marmite. Either you love Microsoft Word, or you hate it. I personally can’t even look at that smug blue ‘W’ without feeling a wave of slight nausea. The alternative for most people is LaTeX, which is a typesetting program. Essentially the document is coded in .tex format, press a button, and out pops a beautiful pdf. Figure, table and page numbering is automatic, and floats actually stay where you put them. There are lots of different versions of LaTeX that all essentially do the same thing so have a search around. My interface of choice is TeXWorks, but lots of other people in my office use TexShop. Bear with the initial steep learning curve of coding in .tex and you’ll be thankful when it comes to writing up. For thesis-writing, you can use a preformatted template or make up your own.
2) Detexify
To write symbols in LaTeX, you have to use a small snippet of simple code. E.g., ≥1 is input as $\ge$1, ∑Fe is written as $\Sigma$Fe. Most of these are pretty intuitive or straightforward to lookup. But what about those annoying symbols you don’t even know the name of? This is where Detexify has saved me a lot of time. It’s a website where you can draw a shape in a box and it will return the likely symbols and corresponding LaTeX codes. N.B. Helps if you can draw.
Detexify: find that elusive LaTeX symbol code. Does help if you can draw…
3) Bibdesk
Bibdesk is an open source bibliography manager. On a simple level, you can use it to log and link to all the papers you read. Where it really comes in handy is when used in conjunction with LaTeX. Linked to a .tex document, Bibdesk will automatically format citations and compile a reference list in your final .pdf. Other options that do similar jobs include EndNote and Mendeley.
4) PDF to Word
LaTeX outputs to pdf format. If your supervisor refuses to read anything that isn’t in Word then you need to find a quick and effective way of converting between the two. The best that I’ve found is ‘PDF to Word‘ by Nitro Cloud. It preserves most formatting, symbols and tables, but struggles with figures, so I generally work with a text-only version (just comment out figures in LaTeX). You get a small number of conversions for free, and then another five a month if you sign up to their mailing list.
5) R
R is a powerful statistical and graphics program. I can’t vouch for the pure mathematical side of things, but I found it an excellent application for making plots. Excel is fine for messing around with data, but I always use R to make the final version of a figure. It gives you a lot more flexibility in terms of graphical parameters and customised plots, and you can easily output as .eps, an image format required by many journals. Other non-Excel options for graphing include GMT (see #9) or Matlab (needs an expensive licence).
Scatterplot made using R (shows whole rock analyses of lavas from the Lesser Antilles island arc – data from the Georoc database [see #10]). Credit: Charly Stamper
6) Textwrangler
TextWrangler is a free text editor for Mac. Does essentially the same job as the default ‘TextEdit’ application but features advanced ‘Find and Replace’ options, line numbering and other formatting options that make it ideal for creating and modifying text-only input files.
7) Tetlab/Trinity
I used Tetlab to create all of my ternary plots. Input is via text file so it’s simple to import from Excel data; standard output is pdf. Trinity comes from the same developer but adds another dimension to proceedings.
Tetrahedral and ternary plots made using Trinity and Tetlab (if you’re confused about the presence of metamorphic minerals, both of these plots are from my masters project on orthogniesses from Greenland). Credit: Charly Stamper
8) Georoc database
If you use petrology at all in your work, the Georoc database is probably going to save you a lot of time and effort. Georoc stands for Geochemistry of Rocks of the Oceans and Continents, and is a collection of nearly 700,000 published analyses of volcanic rocks and mantle xenoliths. You can search by geological setting, location, rock type, analytical method or laboratory, and data includes major and trace elements, isotope ratios and rock ages. Download as a .csv, save as Excel and plot away to your heart’s content (e.g., the graph in #5).
9) Generic Mapping Tools (GMT)
Generic Mapping Tools (GMT) is an “open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets”. In other words, it’s really good for making maps. Like R, I definitely didn’t exploit GMT to its full potential, but apparently you can make all sorts of jazzy 3D maps and use different projections, as well as the full range of normal graph types. The only downside is that it can be tricky to install if you’re not a wizard with Terminal or similar…your best bet is to ask your nearest friendly geophysicist.
Image made using base map compiled with Generic Mapping Tools, though I cheated by adding some extra labelling using Adobe Illustrator (maps show position of Lesser Antilles island arc and volcanic centres on each island). Credit: Charly Stamper
10) MELTS
The MELTS computer program is used for thermodynamic modelling of phase equilibria in magmatic systems. Originally intended for modelling basaltic magmas, now several variations of the original software package have been optimised for different compositions and pressure ranges (e.g., pMELTS for mantle compositions and Rhyolite-MELTS for evolved systems). MELTS lets you take a starting composition of your choice and model equilibrium and fractional crystallisation at different P, T, water contents, oxygen fugacities – pretty much whatever you want. Here’s your chance to do all the experiments you never had time for, though as with any model, you don’t have to take the results at face value.
Screenshot of the MELTS interface on Mac using X11. Credit: Charly Stamper
Steffi
I would add Zotero as a wonderful reference manager on it’s own that can also be used with Emacs/Latex through zotelo (https://github.com/vitoshka/zotelo).