Organizing your research: tips for young researchers, PhD and master’s students.

This article is written in collaboration with fellow amicable scientist Steffen Plunder.

With Marie Kondō gaining so much popularity by teaching people how to organize their houses etc, I think we can also benefit from some organizational tips when it comes to research. Just like regular maintenance of your house/room requires effort and time, this might seem like some effort in the beginning but might do wonders in the long run.

I recently started my PhD and was very happy to receive many tips from fellow PhD students.

  1. Organizing the research papers you read/publish using Zotero/Mendeley: Zotero ( ) is free to use and my personal choice. Here’s the link for Mendeley ( ) which would be an alternative. You can also sync it with your internet browser. The website explains its features, but I would like to list a few of them here as well:
    1. If you are reading a paper on your web browser and have synced Zotero application with your browser, you can just click on Zotero (on the toolbar of your browser) to save the link for future reference under the category of your choice.
    2. If you instead prefer to download the papers you are reading, you can just drag and drop the pdf in the Zotero application on your computer. It will automatically recognize the title of the paper, have all the references including the code for BibTex (for LaTex users).

    You can also add comments about the paper, why you found it useful etc. This is great for people who like to read a single topic from multiple sources. 

    LaTeX users: Install the feature “better Bibtex for Zotero”. You can export the BibTex file corresponding to a paper and copy-paste the contents to use it in your Bibliography. It even has fun features like pushing reference to your current tex document, where it inserts the citation exactly where the cursor is.

  1. Maintain backups:
    Always sync your important files on a cloud service (like google drive, Seafile, Nextcloud, Dropbox, ownCloud etc) so that you never lose them in case of cyber disasters.
    If having files in a cloud is no option for you, use manual backups.
    1. Check if you could support a history and enable it.
      This allows you to recover accidentally deleted files and sections. Most cloud services offer a 30-day recovery option.
  1. Use version control systems for your source code.
    Some code changes might introduce bugs which come to the surface much later.
    To avoid redoing things you already did, you should use version control systems, such as ‘git’. Of course, you can keep millions of folders for each essential change, but tools like git are more effective at doing this for you!
    It also is great for collaboration, since it ensures that changes are merged correctly.

    The typical git workflow has three components:
    i) Pull changes from the remote online repository (if needed).
    ii) Add files and commit changes to the repository.
    iii) Push changes to the remote online repository (private or public, your choice).

    You can use git with a graphical user interface or in the terminal. The best place to go to download and learn about git is:

    A terminal-based tutorial is here:
    These instructions should also help you to understand how to use graphical user interfaces.

    As an online repository, there are several options, for example, or . Both allow private and public repositories and have many nice advanced features as well. Check which one is used by a project similar to yours.
    If you are in doubt, consider using GitHub. An alternative to GitHub is Codeberg ( It is a non profit EU based git service.

    Tips to not be lazy:
    1. Integrate git into your editor! Many development IDE and Editors have git plugins, Visual Code, MATLAB, Qt Creator, Atom, …
      Having git always one button away will help you use it consistently.
    2. Commit often, at least after every programming session.
      For bug-tracing this is essential, it also serves as a changelog for you, since each commit needs a small note about the changes.
    3. Don’t get frustrated if git complains. Sometimes git does not allow you to update your code, since there are conflicting files. This is a feature and prevents you from having an inconsistent code-base.
  1. Maintain a communication protocol/ research diary which can be shared with your supervisor/ collaborators on a weekly basis. Here is the link to a detailed article on how to maintain a communication protocol by the young assistant professor Sara Merino Aceituno (  I highly encourage you to read it.
    This is especially useful for people in theoretical fields, where you might be spending most of your time reading things. It helps you keep track of what you did in the past. It can help provide a better perspective on your research, especially when you are stuck and upon retrospection feel like you have not done anything in a particular month.
  1. Learn how to write: Most science programs do not teach you how to write research papers. Your research results could be exciting for you, but you waste its potential if you cannot write it down in an interesting and understandable way.

    Different disciplines follow different guidelines, so keep that in mind when choosing a book. A nice and general book for scientific writing is Michael Alley’s “The craft of scientific writing”. It is quite fun to read and not much effort.

    For advanced writers, guides like “The Elements of Style” can improve your writing.
    Last but not least, reading is the best way to become a good writer.
  1. Separate work from work-related activities. The following article by Prof. Daniel Nettle is a very motivating and useful article with some more tips. ( ) I found the tip about separating “ Work “ from “Work related activities” very useful (Pg 2, Lesson 1). The author explains how we must do at least one hour of “work” everyday which excludes “work related activities” like answering emails, typing up etc. 
  1. Keep track of time. During your PhD, time will fly without any notable progress in your work. A timekeeping app, like for example Clockify, can help to learn from your past and avoid ineffective work patterns. It also motivates you to think constantly about what you want to achieve in the next hour. However, we just used it for short time periods to assert how we spend time on which tasks.

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