Going back to just about 20 years ago, a researcher’s job was so much more complicated than it is nowadays. Of course, if we just think about the pure research being carried out, not much has changed, the limits of knowledge are still being pushed, little by little every day. However, the tools accessible nowadays might make any researcher of past days feel just the tiniest bit of envy; and I will start with perhaps the most important development: The ability to access any publication in no time through this thing called the internet. Long gone are the countless days spent in the library looking for that one paper and which you desperately needed.

But it does not stop here. In this posts I’ll present a collection of tools I use to make research easy and enjoyable.

Reference managers

If you do any piece of writing which involves any sort of referencing, this tool is a must. I’m not necessarily recommending one particular manager, I’m recommending that some sort of refencing manager is used. Seriously, there is no excuse in this day and age not to use one. The “I’m not good with technology” line is not really holding up, because we now have “plug-and-play” referencing managers which don’t require any special set of technological skills, other than knowing how to install a piece of software and a browser plugin.

How does this thing work then?

The philosophy behind a reference manager is quite simple: First, you build your own literature database in one place. You can do this in many ways; One can manually add entries, but let’s face it, that takes time, and it’s not really exciting. In order to efficiently add entries to your database the easiest way is to use the provided web browser plugin, which, with the power of one click can add the papers to your database, filling in all the relevant fields. Then, as you write, the reference manager, well…manages everything in an elegant and easy way. Any modern manager will have a plugin which integrates with your text editor of choice. You can then add your citations automatically, either in-text or parenthetical. The best part, the manager does it all for you, in the citation style required by the task at hand.

If you constantly have to switch between APA, IEEE or other various citation styles then this will be a total life-saver. Oh, did I mention that they update automatically? For instance, let’s say you use a style which uses numbers for in-text citations. We all know that they can very easily get out of control, especially if you want to introduce new citations. Obviously you’d have to update all the subsequent ones very carefully. And that takes time… a lot of time which can be used for having some more coffee. A manager can therefore completely eliminate these wasted times and on top of that, reduces the chances for human error to a minimum.

And now really the best part, is that when you’re done writing, a reference manager will generate your entire bibliography automatically. How cool is that, there is absolutely no more time wasted with sorting all your references alphabetically, or trying to format them correctly for the referencing style being used.

You can choose between a number of well-known managers such as Mendeley or EndNote. However, My reference manager of choice and my recommendation is Zotero. This will offer you just about anything you need for creating comprehensive databases. What I like the most about Zotero is that it is an inherently simple a tool to use if you just want to get started with it, but it can offer some really amazing advanced tools for paper storage, bulk editing, integrations for just about any editor or web browser. And if you can’t find a tool that suits you, well, you might find a 3rd-party plugin, or might as well go all the way and create you own plugins. Zotero is Free and Open-Source.

I get around the limited storage by storing all my PDF files in a shared cloud folder and then link Zotero to this folder, instead of storing the files directly in Zotero’s storage. I used the guide presented here as a starting point. There are a number of advantages linked with this method, but the main advantage is that one can just open a paper on any device, highlight, annotate, and these changes will now be stored on cloud.

A reference manager is indeed my most recommended tool to anyone with any skill-set. Whilst the following tools which I’m about to show may require some more skills in order to be used efficiently, referencing managers are easy to use and will save you a lot of time. In a following post, I’ll go into a bit more detail about how I use Zotero to its full potential, and how those advanced features and plugins allow me to always have my library up-to-date and well-sorted.

Taking notes

Okay, here, I’ve tried everything, from paper notebooks to an iPad with different note-taking apps, from Evernote to Obsidian and markdown notes. There is a highly personal element linked with note-taking, what works for me now might not work for anyone else, and it might not work for me in about 2 years. But note-taking is unfortunately one of those staged during research which just can not be skipped.

What about just normal pen and paper?

Yes, I love that, there is nothing easier than just grabbing a pen that’s already thrown on your desk and a piece of paper and start laying some ideas down, or sketch something, there is complete freedom. However, the is one small issue, and that is that once you turn that page in your notebook, well that note is now lost.

We could sure use some modern tech for that, can’t we?

iPads are one of the greatest tools in a researcher’s toolkit. Paired with the pen, they give you the freedom that pen and paper gives you, but you can now store and sort your notes so much easier. Add on top of that the ability to have infinite pages, ability to use different colours, and tons of apps which just offer you countless options for writing, storing, sketching, creating mind-maps and many more. I, however, always defaulted back to the native Notes app which came with the iPad, and that’s because of mainly one thing: the ease with which it launches - when you tap the pen on the screen. This is the closest it will ever get to the good old pen and paper. Yes, it is a compromise, but there are certain advantages which make it worthwhile.

And what about these new Markdown notes all the kids use nowadays?

Well, this an entirely new note-taking paradigm, we’ll go a bit more in depth in a following post, but oh boy what this thing can unlock.

Now I’ve been taking notes in every possible way during my time in university and as a postgraduate student and there is nothing wrong with any of them, as long as you do it. But lately, I found that there is a certain beauty in the simplicity of Markdown. A file which can be written in any text editor, which can still be understood in plain text form, but when viewed through the right lens (i.e., renderer in this case) it looks pleasing to the eye as well. On top of that, you can add pictures, you can sort them in nicely sorted notebooks, and you can have links which take you from one note to another. But the main power is that they are still just plain text files, you can put them up on GitHub and share your knowledge with the whole world, kind of like a personal blog (you wouldn’t be surprised if I told you this very website is written in Markdown would you?).

And the icing on the cake, is the ability to create visual mind maps, by linking notes, tags, categories together, in order to better visualise the entire dynamic of the project at hand.

If you want to try out what all this is about, there are a few markdown note editors. Obsidian is the most popular, followed by Zettlr and Roam Research. However, my Markdown editor of choice is Foam. No other editor gave me the same flexibility and options as Foam. It comes as an extension for VS Code, and that means one thing, it’s Free and Open Source. At its heart, it really is just a bare text editor, but combine that with the power of the VS Code shortcuts, Git integration, extensions, command line, and you really quickly have very strong and robust note-taking system which can take just about anything you throw at it. Again, this system is indeed a bit more advanced, and requires a few skills, such as a basic understanding of Git and may not be easily picked up by someone who has never dived into that side, but it’s at least worth giving it a go. Alternatively, Obsidian would be the best place to start, many people swear by it and I think they’re right. It is an amazing plug-and-play system and will get you started with Markdown notes in no time.

LaTeX - Writing Vs Typesetting?

Let’s face it, if you’ve written anything above 4000 words in a classic word processor you know the struggle. It just does not work after a while. The formatting is all over the place, images are not cooperating, and then it suddenly crashes, taking away all your hard work with it. We’ve all been there. So it should come as no surprise that I’m recommending LaTeX as a tool for writing beautiful documents, where you just focus on writing beautiful content.

Back in the early days of research, if you wanted to publish a paper, you would send a “manuscript” (a handwritten document) to your editor, which would then be made to look good by a typesetter. Nowadays, journals don’t really do that any more, it’s more of a responsibility of the author to format their documents before sending them for review. But all that can now be avoided. You can again focus on just writing to content, and let LaTeX take care of the typesetting for you.

LaTeX is an amazing tool, which goes back to the early days of computing. It works somewhat like a programming language, where you define some initial parameters and then use control sequences to define your chapters/sections/subsections. The best feature, again is that it automatically manages your headings, figures, tables etc. You don’t define the numbers of you headings, but you assign them a label, and each time you need to mention a certain section or figure, LaTeX knows how to number them automatically. How cool is that, now if you want to insert a figure before a bunch of other figures, you don’t have to go all the way back through all the figures and update the figure numbers. Again, this is saving you a lot of time, and ensures that there are no mistakes. Additionally, LaTeX will generate a table of contents and table of figures all by itself, no more manual tweaking of the table of contents.

There are many editors to help you get started with LaTeX, however one stood out as making it accessible to a wider pool of people. I’m not going to lie, LaTeX itself has very convoluted ways of functioning, which is a result of years upon years of adding features to a somewhat shaky base. The learning curve is not smooth, but adding this skill to your toolbox will help you through your entire career. The tool that brings LaTeX to the masses is Overleaf. An online LaTeX editor, with all the functionality needed to get you started. It offers great tutorials and I think you’d be hard-pressed to find a tool that just has everything you need readily available.

Now, even though Overleaf is great, and I fully recommend it, for my daily thesis writing I use VS Code paired with the LaTeX Workshop extension. Now there are a few things to consider here. This extension is not the most straightforward one in terms of user-experience, and it sometimes provides additional frustration. With this in mind, I still chose to go with this workflow because of the numerous VS Code keyboard shortcuts, extensions, and general customisation options. There is nothing you can think about and not have an extension which can do that.

Conclusion

There are numerous tools which can help research become a smoother experience. Whilst workflows are highly personal in terms of which tools to use for what task, there are some categories of tools which just make sense in a modern research environment.

If there is anything to take with you, is that if you haven’t yet, do try using at least a reference manager. Start simple, get comfortable with that and then take it from there, you can always add complexity layers on top of the basic functionalities.