Organise or Die!: creating a personal organisation system for your PhD (and life)


If you’re a PhDer, you know exactly what “overwhelmed” means. Crazy deadlines, an awful lot of papers to read (and that will never be actually read), small work spaces and a life that insists on happening simultaneously.

When I started my PhD I quickly realised that I need an organisation system – otherwise I would be, in short, doomed. After all, a PhD is no different from a big project where you are the manager. And the team. And the client. At the same time.


If your desk looks like this, you might be in trouble.

This week I had the pleasure of giving a workshop to my PhD colleagues showing my paperless project management arsenal. In this post, I will show you the tools I use while I walk you through my workflow. I hope to inspire you to find your own system.

It’s all about the workflow – system comes last

It doesn’t really matter what tools or apps you use because they only make sense if related to your research workflow. So I decided to take some time to think about a workflow that would make sense to me.

To visualise your workflow, an easy exercise is to think about your ideal workday. My ideal workday includes these steps:

1. Good habits;
2. Researching;
3. Reading;
4. Note-taking and annotating;

5. Archiving, indexing and searching.

Epiphany: I need tools to help me keep good organisation habits and ease my researching, reading and writing works while I safely and easily manage my files.


You’re a grown-up, get it together!


The ~best~ tool is a very subjective concept. You can read tonnes of reviews and still, that hype tool might not be for you. To make a good choice, take this into consideration:

  • Time – will this tool reduce or increase the time spent on a certain task? Will you need a long time to learn how to use it?
  • Costs – many tools are free, others are not, and the price spectrum is quite large…
  • Individual needs
    • Do you prefer analogical tools (paper & pencil, classic)?
    • Are you tech savvy and really prefer electronic tools (mobile, computer and other gadgets)?
    • Can you carry it everywhere? Can you open your files anywhere?
    • Is this tool accessible if you have any special needs?
  • Operational system – pay close attention to this, especially if you intend to connect different electronic tools together.
  • Possible ethical constraints – i.e. your university might have some issues with sensitive data being stored outside your country.
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Milena Popova’s gorgeous notebook (pic by Paul Spencer)

As someone that started analogically, I keep on loving paper & pen. So I keep my notebooks and my planner (and my Stabilo pens, just because).

So, I realised that a Hybrid system would be perfect for me:

  • Lovely Paper + Pencil delights;
  • Every day’s e-mail, calendar and Office suite;
  • A task management tool – Todoist;
  • A digital notebook – Evernote;
  • A reference management app – Zotero.

The three apps that compose my organisation arsenal are free-ish – they are free to use with some restricted features or smaller storage space. Check each one’s restrictions and if they suit your needs.

But how these tools communicate with the phases of my workflow?


An example of app/workflow integration, by Chris.

1. A good Project Management is all about good habits

projct-managementGood habits in every workflow include Prioritising, Delegating, Doing and Throwing away. The tools that come in handy to get me on doing things are:

  • A paper planner – it comes in many flavours to choose (e.g. Filofax, DIYFish, Bullet Journal, Chronodex and so on…)
  • Todoistmy digital task management tool, where I:
    • Organise my life and work in different areas, so I can see the big picture;
    • Organise my projects by breaking them into Pomodoro-sized tasks;
    • Keep on top and on track of my to-dos:
      • Breaking the work into tasks help you find out the time needed to finish a project;
    • Create and stick to good habits;

I find it particularly good because:

  • It’s simple, flexible and easy to use;
  • Works on any platform;
  • The mobile app turns a phone into a very powerful organisation tool;
  • Creates alerts and repetitive tasks;

2. The fun starts on the Research

Nowadays you can find good/relevant/important anywhere. Saving what you find out there in one place is paramount.

Evernotemy digital notebook. I have it installed on my PC, mobile phone and tablet, and can also use it on the browser. I also use it to work on non-sensitive drafts (like blog posts). On Evernote, I:

  • Put everything I get:
    • Online articles and blog entries;
    • Brilliant shower ideas;
    • Ideas that wake me up in the middle of the night;
    • Things I randomly remember while doing something else (I’ve abandoned the phone’s memo notes!).
  • Prioritise projects, tasks and readings:
    • I have an Inbox folder on my Evernote, for things I can’t immediately deal with and things to read later.

Evernote is a crazy robust software, with an immense range of features. However, to use the software you basically need to:

  • Create a Notebook, a Note (think of a notebook page; it has different types) and a Stack. Give them multiple names.
  • You can write directly on a Note or add content using many features:
    • Web-Clipper
    • Smart Camera
      • Save pics directly from your phone camera;
      • Works like a tiny scanner;
      • Scan business cards and connect them with LinkedIn profiles.
    • Audio notes from your mobile;
    • Save PDF from the browser.

The software also allows you to:

  • Create Shortcuts to your important notes;
  • Set Reminders to work on a particular note;
  • See the Note History and follow the work’s evolution;
  • Find the relationship between your notes, and between your notes and some information online – using the Context feature.
  • Make simple to-do lists on it if you don’t want an app like Todoist.

Zotero is a free, open-source reference manager – and a library: it organises your academic references and saves a copy of the papers on the cloud. It can be used as a browser plugin, or as a standalone app, or as web version on the browser. When I find a relevant reference, I use Zotero like this:

  • If the reference (paper, book, video, news…) is in the browser, Zotero Connector does the job.
  • Add an item by its identifier (ISBN, ISSN, DOI) – one or multiple entries – in the app.
  • Just drag & drop PDFs into the app. It generates a reference through the file’s metadata and automatically saves the file on the cloud, attached to the reference.
  • If nothing else works, I just do a manual entry.

3. Dealing with all that Reading

As a student, you shall read. As a researcher, you shall breathe readings. You will obviously keep the analogical reading arsenal – physical books/papers + paper & pencil – but some electronics can help.

  • Todoist – if you have a long reading list, you can put this list on Todoist and make each reading into a task, keeping track of everything.
  • Evernote
    • Simple reading lists work nicely here;
    • Not the best PDF reader, but you can annotate PDFs and images there if you want;
    • If you are an e-reader user (e.g. Kindle, Kobo, etc), know that it is possible to send your highlights and comments from the device to Evernote.

4. Note-taking, Annotating and Writing

Summarising your readings and findings is a big part of the process. Think of all the papers – and the thesis! – you will write.

  • Evernote
    • Make your life easier with templates you find online:
      • Calendar/planner (handy if you don’t like paper planners);
      • Project management sheets;
      • Cornell Notes;
      • Book/Paper report record.
    • If you work on a text on Evernote, you can merge and update multiple Notes;
    • In mobile devices, you can entry text by Handwriting.

In this phase, Zotero unleashes its power:

5. Archiving, indexing and accessing

Managing everything you found and did is a very important skill.

  • Evernote
    • It syncs with multiple devices. I can access my notes anywhere. ❤
    • It has a very powerful Search engine that includes:
      • Saving searches that you do frequently;
      • OCR technology that allows you to find text in images, and identifies handwriting (how cool is that?!);
    • Work collaboratively by sharing a Note/Notebook itself or its link;
    • You can also link notes with each other.
    • Tags – very useful to code your notes;
      • you can create sub-tags and groups of tags;
      • you can colour code your tags;
      • it all eases the search process.
    • Password locking and two-step verification increase safety.
  • Zotero
    • It also syncs with multiple devices;
    • Remember, it saves your papers in the cloud – very good backup for your library;
    • Very good sorting and basic/advanced search engines, with the option of saving previous searches;
    • It has a Full-text PDF searching to find anything within the actual document.
    • Organising your references:
      • Create Collections to group items;
      • Tags:
        • It automatically Tags your papers using the keywords;
        • But you can create your own tags;
        • And you can also colour code your tags.
      • Create relationships between items.

Now, the fun is only starting when you find out that these apps integrate with each other and with other popular apps and resources:

Todoist integrates with:

Evernote integrates with:

Zotero integrates with:

It was a long post, but I hope it inspires you to think about your workflow and helps you develop your own system. There are many other tools and apps to explore and that can (also) be quite overwhelming, but this is a way to start. If you have your own system, share it with us!

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