Published January 02, 2016 · Estimated reading time: 7 minutes · Filed under ,

*Originally published in Healthy Inference (Dec 2015).

As epidemiology and public health graduate students, a good number of us spend almost more time on computers crunching data than watching youtube. We all have our favorite data analysis tools installed: R, Stata, SPSS, SAS, JMP, WinBUGS, Matlab… we use Dropbox to sync and backup files, Google Docs to collaborate, Endnote or Papers to manage our PDFs and citations, and Evernote to manage our notes.

But aside from the famous  tools we all know and love, there are a lot of awesome software tools and plugins out there that can make our lives just a little easier. You want to search for 50 different keywords in 50 different windows at the same time? there’s a plugin for that (Chrome). You want to download citations on-the-go? this button is mandatory (Chrome, Firefox).  You want to force that window to stay on top so you don’t have to flip back and forth? download a little utility software (Win, Mac).

Here are 5 software tools that have made my life just a little bit better:

*Disclaimer: I’m not in any way affiliated with any of these products. Download any software at your own risk.

(5) Manage your time with Toggl

My to do list today.

My to do list today

Time-management is a critical skill for any graduate student. Fortunately over in Purvis Hall our calendars are organized, our to-do lists are all checked off, and the most frequently heard statement is, of course, ‘why do I have so much free time?!? I need more things to do.’ But let’s say the impossible has happened and with your dozen projects managing time is getting a little tricky, there are millions and millions of tools out there that can help you out.


Toggl (Free Edition | USD $5/monthly subscription | Win, Mac, Linux) is one of my favorite tools for both time and project management. Easy to use and intelligent, Toggl allows you to record and track time spent on various projects. My favorite features include the ability to set defined projects, comprehensive reports across various time-frames, and the little, inconspicuous reminders from the software to keep tracking time. If you work with other project management tools such as a Trello, Toggl can actually be integrated to track the timing of tasks. The software also comes with a mobile app version which syncs across platforms. The major drawback of Toggl is some pretty useful features such as billable rates and task-based estimates are price-locked.

(4) Brainstorm with CmapTools

I used to think ‘mind mapping’ or ‘concept mapping’ or whatever else people call those squiggly intertwining lines with words sprinkled across them was for the aesthetically-inclined. Pretty, but not really relevant to my line of work. However, a workshop I took as part of McGill’s Graduate Education Initiative completely changed my mind. When the coordinator told us we’d concept map our own projects, I thought ‘Oh. I should’ve brought some crayons.‘ But in the course of the workshop I learnt how to use concept mapping to actually identify my gaps in understanding (pay attention: PhD students preparing for comprehensive exams). More important, I learnt that concept maps can be made entirely crayon-free.

Entirely squiggle-free!

Entirely squiggle-free

CmapTools (Free | Win, Mac, Linus | Demo) is a great concept-mapping software developed by IHMC, specifically targetted for use by scientists. For anyone getting started on building concept maps, there is great documentation on the site about the theory and how to do so. The software itself is pretty easy to use, and highly flexible, allowing you to customize everything about your map. Cmap Cloud also allows you to share your mind map, perhaps if you are using it as an organizational tool for a project. One drawback is that sometimes the software can be a bit laggy. Nevertheless, if it’s good enough for NASA it’s good enough for me.

Now you can map your graduate mind

Now you can map your graduate mind

(3) Make your self a digital library with Calibre

One of my dreams was to have a great big library bursting with shelves upon shelves of ancient-smelling books. In lieu of that, I’ve settled for a digital library on my ancient-looking laptop. There are plenty of sites such as Project Gutenberg that provide public domain books. In addition, for many more technical books, McGill Libraries lend out or allow you to download Chapters or even full books for your personal use. While citations tools such as Endnote are great for organizing PDFs and workspace tools like Evernote are great for organizing notes. Neither are really useful for managing E-books.


Calibre (Free | Win, Mac, Linus) is a must have software for all bookworms. The software supports more than 22 formats of ebooks (PDF, MOBI, EPUB etc.) and can covert between nearly 16. It has a straightforward interface which allows for management of Ebooks, including adding meta-data and downloading book covers. It’s also great for managing Ebooks on Ereaders such as Nook or Kindle. There are also a lot of plugins developed by the Calibre community that will let you do pretty much anything with your books. The drawbacks for me have been that the software can be a bit bulky to use when compared to the Kindle Desktop App, and the in-application reader doesn’t have a lot of functions. Nevertheless, there’s not much to complain about for a free open-source software that allows you to have your very own library!

Afternoons in the library

Afternoons in the library

(2) Draft your thesis with Scrivner

I think everybody has asked themselves at some point ‘so uh… how do I draft my thesis?’ but for me, the question when I started was ‘where do I draft my thesis?’ There were so many options: double-roll tissue paper, ancient parchment, a note pad, a word-processor, my email composer box, a typewriter in a coffee shop. There were a number of things that I was looking for in whatever tool I’d be using: first, organize a bulky multi-chaptered work without crazy folder schemes; second, track progress with minimal hassle; third, a tool with good integration with citation management programs.

Those status bars! For more see: What I love about Scrivener.

Those status bars! For more see: What I love about Scrivener.

Scrivner (Free Trial | USD $40 one time | Win, Mac), a favorite tool of actual writers is an effective word processor slash filing cabinet rolled-in-one. Using Scrivner you can split a large work into small moveable chunks, from chapters, to paragraphs, and associate files and additional notes with each section. The program also allows you to set goals and targets for each section and follow your progress through time. Finally, you can include citation codes from your software of choice that generate proper citing when the compiled file is imported into a program like Word. The major drawback of using Scrivner is extremely limited ability to collaborate. So once a draft version of a document is complete, you’ll have to export it to Word or Google Docs to allow for tracking changes and feedback.

Moments after I discovered Scrivner

Moments after I discovered Scrivner

Free alternative: A well-known free alternative for drafting is yWriter5 by Spacejock Software. The software is pretty powerful in terms of its features, however, after using it for a bit I found it definitely seemed to be geared for novelists. So unless your thesis has characters and story arcs, some of these tools may not be exactly useful.

(1) Save  your eyes with f.lux

Some time ago I had a little predicament: When working with my laptop late at night I couldn’t stay awake because my eyes would get tired from the screen, but I also couldn’t sleep because the bright screen would be burnt into my retinas. I tried manually adjusting my screen brightness, but then sometimes you forget. Basically, life was hard.

Writing STATA code at 1:03am

Writing STATA code at 1:03am

f.lux (Free | Win, Mac, Linux) is an awesome little piece of software which automatically adjusts screen brightness and hue depending on your location and the time of the day. You have to set the location, if you want to customize your lighting for day and night and the transition speeds, and the software does the rest of the work. As for the drawbacks: well now life is just too easy!

Do you use any of the tools above? What do you think? Is there another software you would recommend?

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Permanent linkMarzieh Ghiasi

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