Nine of the Best Apps and Websites for My PhD Workflow

From the start of my PhD I have tried a range of applications and programs to help facilitate the process of carrying out my research. In this post I have curated a list of the top nine I use which have stood the test of time.

I’m not going to beat around the bush; if you're looking for the best apps that I use virtually every day, if not every week, in carrying out my PhD, then look no further!

They are in no particular order.

1. Zotero

Zotero is one of the workhorses of my workflow. It does the initial heavy lifting of importing any references directly in from my Chrome browser using the Zotero Connector plugin. When I first started using it I paid a fee to sync across platform (about £40/year) but I’ve since stopped paying and just store it locally. I only need to use it on one computer and I make sure I back-up my database at least monthly.

I use the additional citekeys plugin, which means I can set manual bibliography reference keys to use across any writing. It can integrate with Word if you need; I do also use this function.

It’s super easy to use. You can set up libraries and tags, though I use it at its very basic; import -> export with some tweaking of reference data and citekeys as needed. Zotero is actually incredibly powerful and had I known how it works from the beginning, my PhD may have started out differently. I don’t think most people know how it can work, so I’ll post about this at a later date!

2. Microsoft Office Suite

I mainly use Microsoft Office products (Outlook, Word, PowerPoint and Excel) because I have to rather than I want to per se. I’ll break these down individually because they each hold different and important roles.

Outlook

Because our university uses Outlook to process official emails, that’s where all my email communication and calendaring goes. I mean, I feel it’s kind of the same as any other options, functionally. What really annoys me is, because it’s semi-controlled by the institution, it won’t integrate properly with apps like ToDoIst. So yes, it works, just not as well as I like. I’m kinda locked into this one.

Word

We can’t escape Word (or a freely available equivalent). Whereas only some publishers will accept LaTeX files, all will accept Word files. I must admit, despite using a plethora of other word processing apps, Word is still the most user friendly-keep everyone happy-supervisors can use it…-option. As a text editor, it’s just generally nice to use.

PowerPoint

One of my supervisors’ favourite things to do is “create a slide deck with all your results so we can pick out the important things and see everything in one place”. Now that I do this, I do see the merit in it. Like Word, Powerpoint is also incredibly user friendly and easy to share in discussions with others. Hence why it is the default choice whenever you’re asked to do a presentation.

It’s also pretty convenient when you need to make a poster. There are however quite often formatting issues if pdfs aren’t involved.

Excel

I don’t know of another data entry program that works as-good-as or better than Excel (other than Google docs and other similar free ones). For digitising a lot of experimental data and getting it into txt files, it’s perfect. It’s handy sometimes to do quick calculations or graph things quickly. Excel is another one of those programs that is incredibly powerful once you understand how to use it properly (and I don’t). With moves to have open science, Excel is poo-pooed as an analysis tool so I don’t use it for data analysis.

Microsoft Office is £60/year for a personal license, but if you’re a student you can likely get it on your own PC through your institution.

3. TickTick

TickTick is my app of choice for task management. To be honest I tend to love it, use it for a while, then get overwhelmed, hate it and stop using it. I’m in a hate it phase right now.

I do find it a bit clunky to use, though not as clunky as ToDoIst. I feel that there is a bit of a divide in the style of knowledge and task management apps and that is ‘Notion-style’ and ‘Obsidian-style’. TickTick falls into the Notion-style which is why I don’t think I get along with it as well. There’s just something about it, that doesn’t click with me. I find it good for a specific purpose e.g. planning out the order of experimental steps, but on a day-to-day basis, I need something much less rigid. Does that make sense?

I paid for TickTick Premium (Referral Link for TickTick) with was $28/year to get the full calendar and filter functionality. Not sure I’ll pay for another year though.

4. Web of Knowledge

Web of Knowledge or Science is my go-to academic paper search engine. It’s not the only one I use (nor should it be because it’s biased), but if I need to search for literature, this is where I will start. I used to use Scopus, but for some reason I’ve graduated away from it. I like how easy Web of Science is to use and find papers.

Web of Knowledge I think is only available through an institution whereas something like Google Scholar is free.

5. Obsidian

Aaah, where would I be without Obsidian? Lost in the fog of doom, I suspect. I use Obsidian to bring everything together and as a one stop shop for taking notes and writing things down. Here I can take notes on papers, connect related notes, pull up lists of papers and start to build ideas for writing; like this blog. It’s the first program for me that solved my problem of notes, notes everywhere. And lists, definitely lists everywhere too. Now I have one place to store all my bits of everything. With its powerful search engine, I have my own personal Google.

I’ve been using it for about 7 months now and it’s only just starting to reach some kind of critical mass. I think it’s a lot of work to put it together and get it working how you want, so it’s not for the feint of heart. But it’s worth it; when you’re trying to remember what you learnt about something and you’ve already got a note about it, written in your own language.

You can take a tour around my vault setup over on Medium, along with my top 3 favourite Obsidian community plugins that I use for my PhD.

I pay to sync across devices which is $8/month but there are ways around this such as using Github. I like to think of it as supporting the developers to some extent.

6. Overleaf

I started using LaTeX pretty early on in my PhD. I fell in love with the visual appearance of a compiled LaTeX document. It just seemed so much nicer than anything I could produce in Word.

Although I do my writing outside of OverLeaf at the moment, I aim to publish my thesis using LaTeX. I started using other LaTeX editors but Overleaf dwarfs the competition with usability, functionality and warmth!

Therefore, personally I love Overleaf. It took me a while to set up my thesis document and chapters, but now that I have, I can’t wait to get back into it again and putting finished chapters together.

If you pay yearly (there’s a student option) then it will sync with your Zotero database and you can collaborate with others. But since my supervisors don’t know how to use LaTeX and I had issues with random things appearing in my .bib file that I just couldn’t work out how to get rid of, including the slow updating rate, I just use the free version. It’s just as easy uploading a manual bibliography file at the end. I use all the same citation keys throughout my writing so it’s super easy to do.

7. R and RStudio

R and the interface editor RStudio (seems to have changed to ‘Posit’ recently 🤷‍♀️) are two other workhorses of my PhD. This is where all my data analysis happens. I started by using scripts within RStudio but then I switched to visual RMarkdown and what a difference that made to the usability and friendliness of using R! I use these both on an almost daily basis and couldn’t do my PhD without them. Best thing is they are both free and almost every academic uses them to some extent.

[Note: It looks like 'RStudio' is making moves to integrate with Python hence the name change.]

8. Scrintal

With the advent of Obsidian Canvas, I don’t use Scrintal so much anymore but it revolutionised how I put my literature review together. It allows to me to visualise how everything fits together which was a game-changer for me. I do still use it to map out projects and research papers when I need a ‘quieter’ space to work. It’s nice that it’s separate from my Obsidian. I tend to just go for ‘atomic notes’ on here rather than longform content.

I’m an early subscriber for this one, so it costs me $5/month.

9. Inkscape

Inkscape is a super duper free art editor. I’m still getting to grips with how it works, but it’s pretty powerful. I’ve used it to create diagrams for posters before as it has some neat ‘expanding’ effects which work well for the concept I need to illustrate; you can follow what I did here.. I don’t find it that easy to use. If I want something super simple, I’ll still head to Paint!!

Well there you have it. My list of 9 apps that I use regularly or have a pivotal role in my PhD workflow. Do you use any of these? Do you have any other suggestions?