Advice for the inexperienced PhD: Helpful applications

Since I began my PhD I have been compiling a list of advice either given personally, or which I have found online. The list is long, so I decided to start a blog to compile the advice into a series of posts. This is the first in the series – about non-technical applications that either I use, or hope to learn to use.

Reference management

I would be lost without reference management software. I recently submitted a 10,000 word proposal, that at one point had over 100 references, in the numbered format. I could not have kept track of what was what if I were to do so manually. I cannot comprehend writing an 80,000 word PhD thesis and manually inputting references!

Education Professor Pat Thomson suggests it too: “The key issue is of course not what type of software you use, but the fact that you use it, and use it straight away. It is a real drag going back to the things that you’ve read to enter the details post hoc. Get into the habit at the start of entering everything you read in your chosen system.”

And this great tweet:

You can probably start to see how important this is! I use EndNote, mostly because I can access it for free from my university library, and I knew how to use it before beginning a PhD. There are a number of other programs; Wikipedia even has a comparison of reference management software. Check out what your library offers, and chances are, they will provide training too.


I have been using Evernote since the beginning of my PhD, at my supervisors suggestion. It is where I have been compiling this ever-growing list of advice. You can create different notebooks and notes within each of those. There is an extension for browsers, allowing you to ‘clip’ text and images from websites directly into Evernote. You can also store PDFs. What I find most useful is that you can sync your notes across computers and mobile devices that have Evernote installed, or choose for notebooks to be saved as a local-only folder on your computer. These features are free, however there are more available via subscription.

File storage

I store my day-to-day files in Dropbox. This enables me to sync between my uni computer and personal laptop. I have the app installed on both, but you can also access files via the web. There are privacy concerns raised by many about these kinds of programs, and like anything on the internet, you should be aware of what you upload. Uploading identifiable participant data, for example, may violate your ethics approval. However for drafts of a paper, or copies of articles, I find it very useful. You can also share folders with other Dropbox users, such as collaborators. There are many other popular cloud storage programs including iCloud drive, One Drive, or Google Docs.

File backups

After school I worked on an IT help desk and was regularly on the receiving end of many an angry person who had inadvertently deleted their files. If it was on the network, we kept backups. However for some reason many people kept their most important files on their hard drive, without a backup, and when deleted, were rarely recoverable.

I am now a little obsessed with backing up my data. All my study data is stored on the university network, which is backed up by the uni. I copy updated non-participant data files to Dropbox at the end of each day. This syncs to my personal laptop not only as a backup, but so I can work on the files at home. These files are also stored on the web on Dropbox’s servers. My laptop backs up to Time Machine every hour that it is turned on at home. I also regularly create a full backup of my laptop to an external hard drive and keep it in a safe place. I am very methodical about how I do this, so as not to loose track of what is the most recent version of any file.

My advice is to think about how you backup your data. Is it kept in multiple locations? If your house burnt down, your hard drive corrupted, or your cat knocked an entire bottle of water on your laptop, would you loose all your data? Are you methodical about how you organise your backups?

Organising your writing

One of the PhD students in my lab has recently started using Scrivener. He has found it incredibly useful for writing and organising the elements of papers. It has a 30 day free trial and then must be purchased. I’ve downloaded the program but haven’t given it a go yet.

Organising ideas

I used MindMapple during my honours year to organise topics for a systematic review. I’m yet to use it for my PhD, however it may be helpful in the future. There is a basic version, and a Pro version which cost around $7. A word of warning – if you have lots of concepts mapped out, it is much easier to use if you have a large screen. Otherwise butchers paper and post-it notes may be a better option!


There are a plethora of reminder apps available; how useful they are depends on your needs and whether you want to pay for the privilege of using them. The Reminders app built into Mac & iOS devices is sufficient for me, for the times I want an alarm paired with a reminder. I have a paper to-do list for the rest of my reminders.


All university meetings are scheduled through Outlook, so I use that on my uni computer, as well as the free Outlook app on my phone. I also have a day-to-a-page paper diary that I use to schedule my time and break down my day.


As with the calendar, my university email is run through Outlook. I have both a student and staff account and I have them both added to the one program. This puts all my uni emails in the one spot. At home I use Apple’s built-in Mail and iOS app, with my personal email and both uni email addresses. Helpfully, all of my accounts are able to be setup with imap, so they are synchronised across devices; if I delete an email on my phone, it will have been deleted on my university computer too.

What applications do you use to help manage the day-to-day aspects of your PhD?

Other articles in this series


Self development & promotion


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