10 Software Tools For More PhD Productivity And Less Headaches

PhD productivity is a common struggle among PhD students. We think that the right software will improve our productivity. The truth is that we spend too much time figuring out what the best tools are. Let’s fix that.

I started my PhD and I had new tasks that required software tools. I thought that using the right software would keep my PhD productivity high. But there is so much out there to try. Different programs, versions, prices, platforms and on and on.

I started trying so many alternatives for project management, file synchronisation or handling my literature. I spent so much time trying software that my PhD productivity went down. I was keeping myself busy with trying software and reading reviews of tools.

If you are a nerd like me you might enjoy trying new software for a while. But if you are normal, you might find it a pain in the ass. If you want to move fast in science, figuring out the best software for your tasks is a waste of time.

Allow me to use a bit of business jargon here.

Focusing On What Matters In Your PhD

A baker makes bread. His primary process (his core business) is to make bread. One of his secondary process (what enables the primary process) is to clean his bakery. Having a clean and tidy bakery allows him to make bread. A clean bakery allows him to get a quality certification that guarantees the hygiene in his business.

If the baker spends most of his time on his secondary process, cleaning, he won’t have much time left for making good bread. His business will suffer.

As a PhD student your primary process is to do science. Software is a secondary process, it enables you to do science.

You have to spend as much time and mental capacity on your primary process, doing good science and as little as possible on your secondary processes.

I want to help you to discover the best software without having to wast time finding it. You can have a bigger impact if you use that time for real science.

Let’s say again now with using the style of The 4 Hour Work Week. Being efficient at secondary process tasks (like trying new software) is a waste of time. You want to be efficient effective at your core business (doing science).

Do you see the difference between efficient and effective? When you are effective at doing science your PhD productivity goes through the roof.

Yes, that’s cute! But at the end of the day you have to use software, right? There’s no way out.


So how do you decide what are the best software tools for your PhD? Are there any rules of thumb to choose software for your PhD?

Since I am asking it, then the answer must be yes, there are some rules of thumb. Duh!

3 Rules Of Thumb To Choose Software For Your PhD

a. Choose simple software

Forget software with a gazillion functions. Look for simple software. So simple you could use it in a gazillion different ways.

b. Choose the software your colleagues choose

This makes your life easier when you need to share files or when you don’t know how to do something and need to ask for help.

c. Choose software that syncs your data

Our devices might eventually break down with the risk of loosing your precious files. Use software that syncs via Internet your files across devices. Even better, go for those that also store copies in the cloud.

OK, so far so good. You already know what to look for in a software tool. This should save you some time that you could use for real science.

You know what could save you some more time? Getting a list of the software that best fits that criteria and that you will need for sure during your PhD.

Let me introduce you to 10 software tools you will use most of the time. Not only this, they will make your life easier and painless (at least from the software side of things).

10 Software Tools That Boost PhD Productivity

Task Management (aka to-do list), Wunderlist

I am talking about PhD productivity here. Therefore I should start with the software tool that always comes to mind when thinking about PhD productivity: a to-do list software.

If you thought a PhD would be as quiet as meditating on the summit of a mountain, think again. We receive daily lots of inputs. Do this, send that, prepare that. Add this figure to your paper. Send reminder to boss. Register to the course Literature Review Boot Camp.

The best way to keep track of what to do is our good old friend to-do list. If you are old school you might go for a piece of paper. If you are a bit hipster a Moleskine could be your choice. If you want to go paper-free, you have to try Wunderlist.

Wunderlist is simple, it just keeps a list of tasks. You can group them, for instance if they belong to the same project. You assign (or not) a date to your task. You have an automatic list with delayed tasks and those you should finish today.

Wunderlist syncs your to-do list between devices (Windows, Mac, smartphones, tablets, web browser).

I dump all my tasks in Wunderlist, both private and work related. Since it works everywhere, I can check my work activities in my work PC and my private tasks at home from my Macbook.

Wunderlist is (a) simple software that (c) syncs your data.

Download Wunderlist here

Literature Management, Mendeley

During your PhD you are going to spend a lot of time doing three things: reading papers, reviewing literature and formatting the citations in your publications.

Mendeley can help you with that. It’s quite simple and it syncs everything to the cloud and between computers (so your papers are not lost when your computer breaks down).

Here’s how it works. You download the PDFs of the papers you want to read. You dump them in Mendeley. Mendeley annotates all the title, authors and other info. It syncs the papers to the cloud and other devices. When you are writing your paper, the Word or OpenOffice extension allows you to insert your citations in the correct format of the journal you want to publish in.

And that’s it. No hassle.

Mendeley is (a) simple software, (b) that colleagues use (in my case) and (c) that syncs your data.

Download Mendeley here

Handling Information Deluge, Evernote

Here’s one of the must have software tools for PhD students. It’s worth every penny. But wait, Evernote is free. Even better!

Evernote does two difficult things in a simple way. It stores all sort of information you throw at it and it finds this information when you search for it.

Forget about bookmarks in your web browser, a folder with photos and screenshots, text files with your notes or documents with drafts.

Evernote creates notes with whatever you find on the Internet, with screen captures, with photos from your phone, with PDFs or simply those you write yourself. Everything in one place. And when you look for them, you just need to search for them a-la-Google.

Evernote is (a) simple software and (c) it syncs your data.

Download Evernote here

Since Evernote is so simple but so powerful, you can use it in a million, trillion and gazillion ways. If you want to learn how to squeeze all the juice out of Evernote, please read Evernote Essentials. Evernote Essentials is the Bible of Evernote.

Get Evernote Essentials here

File Back-up / Sharing / Sync, Dropbox

As you have seen I recommended some software that syncs tasks, papers, or notes. How do you sync other types of files like code, photos or documents? The answer is Dropbox.

When you install Dropbox in your computer it creates a folder called ‘Dropbox’. The contents of this folder are sync’d with ‘Dropbox’ folders in other computers or Dropbox apps in smartphones and tablets. Additionally, Dropbox sotres a copy of your files in the cloud to make sure you don’t lose a file under any circumstances.

How to use Dropbox for your PhD? Easy, drop all your PhD files and folders inside the ‘Dropbox’ folder. Install Dropbox in other devices. Sync. Done. No more “I can’t work on it because the file is in the other computer”.

Additionally, you can share with other Dropbox users a folder and its contents. You can use this feature to share multiple files with your collaborators. Remember when your email provider said you cannot send that files because it’s too big? Dropbox fixes that.

Do you know a real PhD productivity killer? Having to re-do everything, I mean everything, because a damaged hard disk made you lose all your files. Dropbox would save your ass in that catastrophic event.

Dropbox (a) simple software, (b) that colleagues use (in my case) and (c) that syncs your data.

Download Dropbox here

Using Software From Other Operating System, Virtual Box

Now we are going to get a bit computer nerdy, but do not be afraid.

Here’s a common pain with software in science: the program you want to use cannot be executed in your current operating system (OS; like Windows, Linux or Mac OS).

When does this happen?

  1. With legacy software, aka freakishly old software. It hasn’t been updated anymore and it uses some old libraries, so for instance, it can only run on Windows 95.
  2. Software developed by other scientists that is not compiled in your SO. So that good willed scientist built a program that is the golden standard in your field, but it only runs in Linux, and you have Windows 7.

The simple solution here would be to buy a computer and install the SO you are missing. Or…you virtualise a computer using VirtualBox inside your current computer. Then you would install the needed SO in that virtual computer and the desired software.

With VirtualBox you can have as many virtual computers with different SO’s as you want.

VirtualBox is (b) software that colleagues use (in my case).

Download VirtualBox here

Writing, Word

Writing papers is one of the important tasks in your PhD. True, most of the time is spend doing real research. But you will show your research to the world with your publications.

Do you know what happens before you publish one of your papers as a PhD? Endless feedback on your draft.

Don’t worry, it gets better as you gain experience. For my first publication I got a ton of feedback. For the second paper just half a ton. And so on.

Now back to writing papers. You have to use a text editor. Since you want to get digital feedback (not unintelligible cramped handwriting on the sides of your printed draft), you need to use the same editor as the person giving the feedback. And it’s going to be Microsoft Word 99% of the times.

So there you go. Get yourself Microsoft Word.

Truth be told, I use also other editors. I like Pages and Evernote for preparing my blog posts.

Scientific fields with a high formula to text ratio in their publications use LaTeX as editor. Social sciences PhDs have recommended Scrivener, which I used to write my ebook 17 Simple Strategies To Survive Your PhD (don’t forget to download it, it’s free)

Word is (b) software that colleagues use (in my case).

Get Microsoft Word here

Handling Data And Plots, Excel

During your research you are going to produce some data and store it as a table. Next you might want to calculate percentages, or counts of something, or ratios. I don’t know, something.

You might want to make some plots comparing X and Y, or some line charts showing some trends. Those plots will be some of the figures in your next publication. I know, Excel images in a scientific paper are not very sexy. But hey, who hasn’t done it at least once in their career?

Excel is (b) software that colleagues use (in my case).

Get Microsoft Excel here

Slides, PowerPoint

Let’s talk now about making slides. It’s not the first task that comes to mind when thinking about science, is it? Well, during my PhD I have made plenty of slide decks. Mostly for conferences or little group meetings.

You know the drill. You attend a conference to present your scientific results. You go on stage. You first slide is on the main screen. Your legs are shaking. Thanks to the organisers for inviting me. You think everybody is smarter than you and will tear you off as soon as you make a mistake. My name is … You feel the sweat drops sliding in your back. The title of my presentation is … Your vision gets blurry. 4 years of work summarised in 20 slides. The will laugh. You pass out.

Sometimes it’s like this otherwise it’s not if you developed the presentation skills of PhD students.

But the important part are the slides. They are made in PowerPoint. Why?

Well, everybody uses PowerPoint. Many conferences only allow presenters to use PowerPoint slides. They say that they cannot guarantee that other formats will work well.

But Julio, Keynote on a MacBook always works well at the first attempt.

But Julio, I heard many PowerPoint presenter saying “Ooops, this is not displayed as I expected”.

You are right, but if you want to present at conferences you have to swallow it.

PowerPoint is (b) software that colleagues use (in my case).

Get Microsoft PowerPoint here

Web browser, Chrome

Browsing the Internet can destroy your PhD productivity. It can also help you find the information you need and answers to some questions.

It’s time to talk about the software tool that is going to help you answer a question. It’s a big question. Probably the most interesting question in the course of your PhD.

Is the new lab intern single?

That scientific curiosity should be addressed. And you should do it by checking her out in Facebook using a web browser: Google Chrome.

Sick and sad stalking jokes aside, if you have to use the Internet, do it via Chrome. It’s a clean, beautiful and easy to use browser. I have used most of the browsers and I can say that Chrome feels like it was developed by people who like to spend time on the Internet.

A last tip: install the Evernote plugin for Chrome so you can create a note from any website directly from Chrome.

Chrome is (b) simple software and (d) better that Internet Explorer.

Download Google Chrome here

Music, Spotify

I don’t know how I would have gone through my PhD without music.

Music to cheer me up on a grey day. Music to focus while writing. Music to keep me awake while doing repetitive tasks. Music to stream to my smartphone. Music to boost my PhD productivity. Music to activate my resourcefulness while programming. Music to survive a PhD.

All this music came from Spotify (and a bit from Youtube). But mostly Spotify. I gladly pay for the Premium version. For me it’s worth it. I got tired of downloading music, and loading it in a MP3 player, and updating my playlists. Spotify was just so convenient.

Let music boost your PhD productivity!

Spotify is (a) simple software that (c) syncs your data.

Download Spotify here

About Julio Peironcely

Julio Peironcely, PhD is the founder of Next Scientist and a PhD by Leiden University. He helps PhD students to stay motivated, be more productive and finish their PhDs. Follow him on Twitter (@peyron) or read more from him on JulioPeironcely.com.


  1. I use most of them, but EndrNote x6 for writing the bibliography and citation which is very convenient. I highly recommend it for you guys.

    • NextScientist says:

      Yeah, EndNote is widely used in Academia. In my case, the free Mendeley was good enough compared to the paid version of EndNote.

  2. qiqqa is nice. I like it so far. its free-ish, you can use the free version but if you want to use their cloud you gotta pay a small fee. Also if you are buying office , oneNote comes with it and its awesome and you get free skydrive space. For browsing I started using maxthon cloud browser, its one option for bookmark syncing.

  3. I use Kanban Tool (http://kanbantool.com) to plan activities and collaborate with my colleagues on research projects. The tool is based on Kanban method, it helps organize tasks, documents and so on. It facilitates cooperation between people that are in different, distant locations as it allows to share tasks, documents and comments.

  4. Dr. M Zahid Khan says:

    Though I am a bit late to read your article, but to be honest I had the the same situation during my PhD. I am gonna recommend it to my research students.
    By the way how could you forget Qiqqa and Google Drive.!

  5. I would also like to recommend another app Proofhub (http://www.proofhub.com/) to plan activities and collaborate with my colleagues on research projects.

  6. Sonia Goopta says:

    Productivity is one such aspect that needs rigorous dedication to meet the deadline. In order to have a great reach of productivity, it is very much necessary to have the main points to be considered, and among all the concerned points, I prefer time as one of the major aspects of a good gain in productivity. To have a good control of time and be specific on that I have specifically use the hours tracking software from Replicon ( http://www.replicon.com/olp/hours-tracking-software.aspx ) which practically manage the time with the tasks management as well. I would like to recommend this software here over.

  7. I was using Mac (sometime Linux and Window) for my Ph.D. Therefore, I used this set of tools that work on all such platforms:

    1) RTextDoc LaTeX editor with grammar checking and BibTex database: http://jwork.org/rtextdoc/

    2) SCaVis to make graphs in EPS format that can be included to my LaTeX documents http://jwork.org/scavis/

    And all of this can be installed using one-click approach using jPort portable desktop (http://jwork.org/jport/)

  8. All of it corporative software. You dont give any reference to open source software. Even a simple browser…. why not Modzilla?, what makes Chrome so special?.

  9. Julio, I spent more than 4 hours on your awesome plug today, all the information is exactly what I was looking for before starting the real work. Thanks for your time and effort and keep it coming 😉

  10. Disagree in you recommendation about Word. Scrivener is far much better, it gives you much better overview, both when you write an article and the final thesis. Of course, you have to you use Word to wrap it all up at the end.


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