Last year (2025), I did my master's degree thesis on Phytoplankton. Before I started writing my research proposal, research paper and coding, I've scoured a bunch of articles and YouTube videos to help me organize my research project specifically in these 4 major areas: a way to organize the papers that I've read, a way to organize my presentation and weekly progress report, a way to organize my research writeup and a way to organize my codes. It took me weeks to finally figure out what works for me and what doesn't. And the simpler the tools are, the better. In this article, I will show you organization tools and template I used to make my thesis writing more organized and efficient.
Organizing my Library
Okay so let's start with the first one, organizing my article/book library. Zotero (Download link) has been one of the most popular research paper organizers that allows you to download, annotate and sync your library to multiple devices. The syncing feature is really important to me because I usually read papers using my tablet especially when commuting or waiting for class. The free storage is quite limited so if you don't want to spend money for the storage, just make sure to disable the "Sync Attachment Files" in the Settings. Otherwise, I highly recommend subscribing as it helps the developers continue improving this app as it is very useful in research or personal use.
Preparing for the presentation and weekly progress report
Ever since I started using LaTeX in my undergrad days, it has always been my go-to formatting system especially in academic settings. Whether a simple assignment, resume or presentation, I always use LaTeX. It might be daunting to use at first, but trust me, when you get the hang of it, it is so much easier than doing it in MS Word. The beauty of LaTeX for me is that it is like a normal HTML code that we can push to git repositories so that we can track the individual changes. Using document tracking alone in MS Word is not as intuitive as git in my opinion.
There are many online editors for LaTeX out there like Overleaf (Website link) which is really helpful if you don't want to install LaTeX libraries in your machine but I think it is much more cost effective and efficient if you install it directly as it allows you to use git and use VSCode to edit the .tex file. Plus, usually these online editors only allow limited compile timeout, so if you are like me, who wants to see the compiled pdf in 'near' real time, then you would want to switch to the installed version.
Okay, so to install LaTeX on Windows, you first have to install MiKTeX (Download link).
Download and install Strawberry Perl (Download link). This is required if you want to use VSCode as your LaTeX editor with MiKTeX.
Next, install the "LaTeX Workshop" Extension on VSCode. See Extension below.
Copy the following in your VSCode settings:
"latex-workshop.latex.autoBuild.run": "onSave",
"workbench.editor.enablePreview": false,
"latex-workshop.latex.recipe.default": "pdflatex -> bibtex -> pdflatex x2",
"latex-workshop.view.pdf.viewer": "tab"
Btw, you can download the Beamer template I used (here). Below is what it looks like once you save the tex file.
Organizing my Research Paper
This is the hardest part to be honest. Took me months to finally be able to write something. Thanks to my supervisor I was able to navigate around this. Because to be honest, even though I narrowed down my research area of choice, sometimes I get swayed to related but a lot broader topics especially when I started reading papers. It is pretty much like reading Wikipedia articles in which the more you read the more you get buried deep into the rabbit hole which leads to no writing at all, just reading. If you don't write what you read it does not help you at all. So at first, I tried to take down notes as I read but then I realized I would have to re-organize and combine these notes again which I will end up doing again when I finally started my research project writing. Which got me thinking, I should prepare my thesis outline ahead of time regardless if I don't have content yet or not. This way I can organize which subtopics to look for and which topics are missing in my report.
So just like what I did in my presentation, I created a LaTeX project for my research project writeup outlining the topics and as I go through reading different related research papers, I write my research project at the same time. Here's my final outline. Trust me, this took a lot of revisions from my supervisor which I really appreciate.
One important detail that I highly recommend is copying and pasting the exact phrase that you referenced in your paper to the bibliography file (just like below) to make sure that you can come back to the specific paper more easily so that you can improve your paraphrasing more accurately. In my case, there are days where I find it hard to write anything but I know that I have to do it so I just paraphrase it using the lamest paraphrase I can just to get by. So keeping these exact word for word reference notes helped me rephrase and refine my sentences more accurately.
Organizing my codes
Okay, so the last one is the coding part. This is actually case to case basis. For my case, I'm using Python so I find it easier to just use Jupyter notebooks to test out my experiments. There are other libraries and tools that I used to easily keep track of my experiment results including MLFlow but I'll probably post in my next blog post.
Hopefully, this is helpful to those people starting their master's degree thesis or to those people who want to organize their research workflow in general.