How to Organize Your Notes for Optimal Research Productivity

When I first started to write notes for my PhD work, I remember trying to keep notes in a single .txt file on my laptop. As new ideas came in, I just added them to the file. Eventually, that file got huge, making it really hard to find anything useful when I needed it. I eventually abandoned the .txt file, losing all that content in the process. Then, I switched over to writing my notes in composition notebooks. The quad ruled ones were and still are my favorite. My note taking was a bit better in the quad ruled notebooks, but I still had the same problem. How could I find relevant notes after I had written them? Once I’ve filled an entire notebook with ideas, diagrams, and results, how on earth do I find them afterward? I basically had to flip through every single page, unless I knew for sure that what I was looking for was near the beginning or the end of the notebook. After years of failed attempts at note taking, I finally realized that the medium didn’t matter. I had the same problem digitally as I did on paper. I needed a system for organizing my research notes.

I laughed when I realized what the problem was, given that I’m a researcher in data science. It is literally my job to make it easier for other people to organize, explore, and make sense of their data. The same principles apply to my own data as well. After coming to this realization, I made it my mission to develop a note taking system that actually works for me. After ten years of trying, I believe I finally have a system that works. It is magical! In this post, I share my note taking strategy, so you can apply it to your own computer science research.

The Key Idea: Focus on Connections, Not Just Content

My goal with note taking is to build a powerful information system to support my research. But how do we structure such a system? To answer this question, consider the structure of two of the most powerful information systems in the world. One is the brain, which contains an interconnected network of billions of neurons used to pass information from one part of the brain to another. In machine learning, neural network architectures try to mimic how the brain uses neurons to build vast networks of information. Another example is the internet, which is an interconnected network of digital information spread all over the world. You can be on the opposite side of the world from me and through the internet you can still read this post. Within the internet, consider Google search, specifically the Page Rank algorithm that made Google famous. The way Page Rank works is it analyzes which webpages are connected to each other through hyperlinks. The more tightly clustered a set of pages are through hyperlinks, the more likely they are to be semantically related. Furthermore, the pages that are linked to the most are likely to be the most authoritative pages within the clusters. In other words, Google exploits the connectivity of the internet to power its search engine. See a theme here? To apply this concept to research notes, we simply substitute neurons and pages with individual notes. In this case, the content of a note matters, but how it connects to other notes (and our brains!) is even more important.

High-Level Steps to Writing Excellent Research Notes

Here is a quick summary of my key strategies for writing great research notes:

  1. Write everything down
  2. Tag notes by category, concept, or theme
  3. Link related notes together
  4. Create a table of contents for each major project

In the rest of this post, I describe each step in detail and provide some helpful tips to boost the utility of your research notes.

Step 0: Choose Where to Write Your Notes

If you do not currently take notes, then you will need to choose a note taking application to write your notes in. My favorite note taking application is Evernote, so I will be using it in all of my examples. However, you can apply these same principles to any other note taking strategy, including paper notebooks. Check out commonplace books for examples of how people applied similar concepts throughout history. However, having access to hyperlinks and search bars makes navigating related notes much easier. Also, digital notebooks never run out of pages! So I recommend going digital if you can.

I wrote up some helpful tips on picking a good note taking app in a previous post. If you already have a note taking app that you enjoy using and it has the features that I recommend, just start there. Don’t delete anything and don’t make a new notebook. Just use the default notebook for now. The beauty of my note taking strategy is that it doesn’t matter whether all the notes are in one place or not. To keep things easy though, we will place them all in the default notebook. If you are a bit more advanced and want a separate notebook to test things out, then feel free to create a new one and change the settings to make it your new default notebook.

The most important part of Step 0 is to be consistent. Keep all of your notes in the same place. For example, I keep all of my research notes in Evernote. For me, if it’s not in Evernote, then it doesn’t exist. This way, I never have to remember where I put my notes. Do you want to migrate to a new note taking app? No problem, but make sure you copy all of your notes to the new app. If you have hundreds of notes this might sound intimidating, but trust me it’s worth it. If you don’t want to do it all at once, then do the following:

  1. Just migrate 5 notes per workday. The most important thing is to be consistent. Do what you know you can handle on a daily basis and do not stop!
  2. Do not tell yourself that you can just “get it all done on the weekend.” Find a way to do the daily migration on workdays only.
  3. For each note you successfully migrate to the new app, delete it from the old app. That way, you always know exactly what still needs to be migrated.
  4. If you are pressed for time, then go down to 1 note per workday, but do not stop migrating! Then, go back up to 5 notes per workday as soon as you can.
  5. If you have more time, try to migrate more notes, for example 10 notes instead of 5 notes. But remind yourself this is just a temporary boost. Go back to 5 notes the next workday.
  6. As a bonus, start tracking your migration using your favorite habit tracking method. For example, you could use a habit tracking app, check off a daily task in your preferred calendar app, cross days off on a paper calendar, and so on. Do what works best for you, but as Jerry Seinfeld famously recommends: don’t break the chain.

This simple trick of breaking big projects down into easy micro-tasks and doing them every single day is the reason why I started this blog. This strategy applies to everything in research, and arguably everything in life. My goal is to show how to apply this method to any and all aspects of computer science research in future posts.

Step 1: Write Everything Down

To build an information system, we need information and lots of it. Also, with an open-ended discipline like computer science research, we never know which notes will lead to new scientific breakthroughs. For these reasons, we need to write everything down in our research notebooks. However, much like how I can’t just write crappy, disorganized webpages and expect to rank highly on Google search, I can’t haphazardly write disorganized research notes either. The information stored within each top ranked webpage has to be organized a certain way for Google to recognize its value. In the same way, each research note has to have a detailed and consistent structure.

My biggest tip for writing detailed notes is to always write the note as if someone else, for example a new student joining a research project, will need to use the note. An even better way to look at it is to treat notes like webpages that someone else might search for online. Is the note content going to help a random person searching for this information online? If not, then it probably will not help you either, at least once the original context is forgotten. Forgetting the context only takes a couple of months, but research projects are completed on the scale of years. Do your future self a favor and write everything down now. My second biggest tip is to write a descriptive title. Imagine all those Google search results you ignored because the webpage titles were too vague. The same holds true for searching your own notes. Again, make life easy for future you and just write the details down now.

I’ve written an entire post on how to structure individual research notes, and describe four types of notes to focus on: ideas notes, process notes, reference notes, and results notes:

  • My ideas notes capture new ideas in the moment so I never lose them.
  • My process notes record step-by-step guides for critical yet complicated research routines.
  • My reference notes manage external resources that I turn to again and again as I do my work.
  • My results notes record the findings and implications of completed research tasks.

If you want a concrete example of how to write ideas notes in a structured way, check out this Evernote template that I made. It provides all the details you will want to track for your ideas. You don’t have to use the whole template, and can complete each part at your own pace. For example, I typically write the core idea down as soon as possible, then add relevant papers and whatnot over the following days, weeks, or even months, depending on how long it takes me to get back to the idea. If you want detailed tips on how to write all four types of notes, please check out the original post linked above.

Step 2: Tag Notes by Category, Concept, or Theme

After you’ve written a new note, the next step is to help your note app understand how it connects to the rest of your information system. This step matters because keyword search is not always that effective out of the box. Unlike bloggers and website owners, when I write notes, I’m just writing my thoughts down, and not necessarily trying to maximize keyword relevance and back links. This is exactly how notes should be written. However, this makes keyword searches over your notes less effective than online keyword searches over websites. That being said, there are steps we can take to make keyword search work better. One step that will definitely help is to use your note taking app’s tagging feature.

The key idea with tags is to include information that you might not include in the body of the note. To keep things simple, I recommend using the following types of tags:

  • Note Type Tags: for the type of note you wrote (idea, process, reference, result)
  • Project Tags: for the research project this note belongs to.
  • Task Type Tags: for the type of work you were doing as part of this note, such as “paper writing”, “thesis writing”, “user study”, “proposal/fellowship”, “job hunting”, “teaching”, etc.

You could also add tags for research areas, such as “visualization” or “databases”, but I would avoid them since different areas may go by multiple names. For example, “database” research could also be “data management” research or “database management” research, or even “data science” research. Furthermore, this content will likely end up in the body of your note anyway and so will be redundant as a tag. Save yourself the trouble and avoid adding these kinds of tags. For conferences, you will probably put the conference name in the body of the note, so there’s no need to add a dedicated tag. The same goes for course numbers if your note is related to a course.

I often like to include tag names in the title as well. For example, research idea notes I might title as “Research Idea: [rest of title]”. This helps me skim notes while reviewing search results in Evernote.

Step 3: Link Related Notes Together

My absolute favorite feature of Evernote is internal links. This feature is arguably the single most important feature for building a robust information system! I prefer to find relevant notes by clicking a couple of links rather than having to use the keyword search feature.

Never used this Evernote feature before? All you have to do is:

  1. Right click on the thumbnail of the note in the notes view on the left hand side of the Evernote window.
  2. A menu should pop up, like the one below.
  3. Click on the “Copy Note Link” menu item.
  4. Paste the link within a different Evernote note as desired.
To get the internal hyperlink for a note in Evernote, right click on the note. You will see a menu pop up with an option to “Copy Note Link”.

When you paste a note link in Evernote, it will look like this:

Internal note links will appear green in Evernote and show the title of the note.

The link will be green instead of blue, and the title of the note will automatically be used to describe the link. As I work on projects, I try to always include links at the top of the note to other relevant notes. For example, if I am analyzing a dataset three different ways, I may make each analysis a separate note, and add the links for the other two analyses at the top of each note. Here’s an example from my own notes. This note is from an old project where one of the main contributions was a literature review:

An example of how I like to include links to related notes in Evernote as I do my research. This example is from a literature review project.

We had to iterate on the clusters of papers we wrote about, and the text for the literature review itself. I kept track of these previous iterations using Evernote links.

However, you may get to a point in your research project where it becomes a huge chore to copy all of the links over all the time for each new note. Furthermore, not every note about a project is relevant to every other note for that same project. This is where the last step becomes crucial.

Step 4: Create a Table of Contents for Each Major Project

There is actually a fifth type of note that I use all the time in my research notes. However, this note type is more organizational than content focused. This is why I don’t include it in my four types of notes. The fifth type I call a “Table of Contents” note. This note is the master list for all relevant internal and external links for a given project. Here’s an example for an old research project:

An example of a partial Table of Contents note from an old project. I used this note to keep track of later revisions for a conference paper.

For this project, I conducted a user study and had many smaller analyses I needed to do using the study data. I made separate notes for those analyses, and linked them in the table of contents. I also had to submit the paper a total of three times, and wrote a lot of notes on how to improve the paper for each submission. I linked those notes in the table of contents as well. As you can see, I had a lot of notes to keep track of for this one project! Furthermore, I did not start my table of contents until after my paper was rejected the first time, so there are older notes that did not make it into this table of contents example. My recommendation is to save yourself some trouble and create a table of contents note at the very beginning of the project, that way you can just maintain the same note the entire time. If you end up having to spend a year or more on a project, then you will be glad you linked all of your relevant project notes in one place.

When writing papers or generally collaborating with other people on a project, I also write content outside of Evernote, such as in google docs or Overleaf. Table of contents notes are also great for capturing these links. Furthermore, if there are specific resources that I need to reference for the project, such as submission guidelines for a particular conference or award program, I include those links as well. Here’s another example for a (rejected) proposal I wrote last year:

A table of contents note that I created to manage various notes for a proposal submission. I use table of contents notes to track internal and external links in one place.

Something I love to do is to add table of contents notes to my Evernote shortcuts. That way I can always go straight to the table of contents for an active project to find a relevant note. Once the project is no longer active, for example once the corresponding paper is finally published, then I remove the note from my shortcuts.

Bringing Everything Together: Some Helpful Guidelines

I provide specific steps above for creating an effective information system to support your research. Although following these steps has worked well for me in the past, you may want to adapt these steps or even create new ones to better suit your needs. Here are the key principles to keep in mind when extending these steps:

  • Write your thoughts down ASAP: It is difficult if not impossible to remember every detail and every outcome from years of research. Even if you choose to write different kinds of notes or focus on different note details, the most important thing is to write down your thoughts as soon as you have them! Write down as many details as possible to capture the full context. If you do not do this, you will hinder your growth as a researcher.
  • Keep everything in one place: If you are like me, then you tend to lose things when they are not in an intuitive place. My life is much easier when I have exactly one place to look for things. Even if you hate Evernote or prefer paper notebooks, I hope we agree that keeping notes in a single notebook or a single app is easier than keeping notes in multiple places.
  • Cluster related notes: I shared three ways that I cluster relevant notes (keywords, links, table of contents). The key idea is for notes that are related to have an established connection that you can use to navigate easily within the cluster. Even if you don’t remember the exact details of a specific note, you may still remember the general topic or theme and can use these connections to find it.


Writing good research notes is all about the connections, how different ideas connect to one another across notes. Connecting disparate ideas together is the definition of creativity and the cornerstone of scientific innovation. If you want to accelerate your ability to make these connections, then you absolutely must organize your research notes! In this post, I described my four step process to organizing my notes, and the key principles behind my organization strategy. Check out the infographic summarizing the steps below. If you want more details on how I organize individual notes, check out my previous post.

Four Kinds of Notes to Boost Your Research Productivity

a snapshot of a note written in Evernote. The note contains a list of quotes about data, science, and knowledge.

I am obsessed with writing notes. I document a lot of my personal and professional life through notes. If I come up with a new research idea, I write a note about it. If I come across a relevant paper, I write about it in my notes. If I find a recipe I like and use frequently, then I add it to my notes so I don’t have to search the web to find it again. Every time I read a new book, I write a note about it, which includes any quotes I liked and my review of the overall book. For example, I just finished reading Digital Minimalism by Cal Newport; here’s a quote from my notes: “A foundational theme in digital minimalism is that new technology when used with care and intention creates a better life than either Luddism or mindless adoption.” [2] I love to play disc golf, and I track all of my past plays using my favorite note taking app, Evernote.

Since I am an avid Evernote user, I share all of my examples exclusively in Evernote. If you are looking for a new note taking app, I share some helpful suggestions on how to pick the best note taking app for you in my previous post.

The Key Idea: Write Everything Down

The main theme behind this post is that for anything meaningful that we encounter in our work, we should be writing it down. For example, with an open-ended discipline like computer science research, we never know which notes will lead to new scientific breakthroughs. If we don’t write ideas down as we have them, then we risk losing them and in turn potential innovations and breakthroughs. For these reasons, I recommend writing everything down as research notes.

Although I focus on computer science research in this post, these ideas can apply to any part of our lives that we deem meaningful. For example, I write notes for all of my hobbies in Evernote. In fact, I often learn new note taking skills through the process of writing personal notes, which I then apply to my research notes. Writing good notes is a transferrable skill that I can use in every part of my life.

An Example Note

Here’s an example of a note that I use every single quarter, and it is just 5 lines of content in Evernote:

An example of a note I regularly use, written in Evernote. The note is about five lines and explains the process for creating a Python3 virtual environment.

This note explains how to create a Python3 virtual environment. I have written a templated example on the first line, followed by a concrete example that I frequently use, and finally a link to the original source of the information, in case I want to review the material. In this case, the source is a page from the official Python documentation. Technically, I could easily look this up online each time I want to create a new Python3 virtual environment rather than writing a note in Evernote, but this way if I don’t have internet access I can still look up the answer in my own notes. You might be wondering “don’t you eventually just memorize how to do this?” Sort of, but I never remember the exact details. Rather than guessing how to do it, or relying on my (often faulty) memory, it’s easier to write it down once and look it up later.

The above note is an example of documenting one of the processes I perform as I conduct my research. By knowing how I intend to use a note, I can structure it accordingly to maximize my ability to reuse it in the future. In this case, by documenting a step by step process for creating a Python 3 virtual environment, I make it easier for myself to create virtual environments later on.  Also, if a student asks me how to create Python3 virtual environments, rather than explaining or demonstrating the steps for every student individually, I can just share this one note in Evernote by turning on public sharing for it and sending each student the sharing link.

Writing Notes for Ideas, Processes, References, and Results

However, not every note should be written as a step by step process, depending on what the note represents. I group research notes into four different categories:

  • Ideas: new research questions or ideas I might want to explore in the future.
  • Processes: a detailed, step by step guide to completing a specific procedure that I performed in the past.
  • References: Bits of information or pointers to information sources that may be useful in the future.
  • Results: A description of my findings after completing a specific research process, ranging from 1 paragraph to multiple pages of content.

I think of Ideas posts as being “before” posts, or notes recording my thoughts before I conduct the research. Process notes are what I record while conducting the research, and results notes are what I document after conducting the research. Before, during, after. In this way, I can cover all aspects of the research process. Reference notes I think of as just-in-time notes, for specific situations that come up frequently but not with obvious regularity. To get you started on writing great ideas notes, I’ve created a template anyone can use, available here. I’ve also made an infographic summarizing the four note types, for easy reference!

The four note types I use to boost my research productivity. Although I provide a lot of examples from my research in computer science, the ideas apply to any kind of personal and professional work.

Writing Process Notes: Another Example

In the past, I wrote abbreviated versions of process notes, assuming I could “fill in the blanks” with my memory and past experiences. However, I have found that I often revisit process notes months or even years after I originally wrote them. By then, I have completely forgotten the original context in which I wrote the note, making the abbreviated version useless. My most vivid memories of these kinds of debacles involved installing the database management system SciDB. I had to re-install SciDB four times throughout my PhD, basically once per year. These were in the very early days of the software, when the installation process was difficult and largely undocumented. The first time, I didn’t bother taking any notes. Installing SciDB took several hours! Unfortunately for me, when I had to install it again months later to upgrade the software, I knew I was in for another multi-hour installation session, but this time I actually took notes. They weren’t perfect, but they had a lot of useful information. Each time after that, I refined my notes. Near the end of my PhD, when I installed SciDB on the MIT servers for the last time, I was able to complete the installation in under half an hour. Here’s a snippet of my SciDB note, to give you another example of a process note:

An example of a more complicated process note from my own research. In this case, I was tracking how to install SciDB in my earlier years as a PhD student.

It’s pretty hard to remember exactly how to do something you only do once a year, especially if it’s super complicated. For example, it’s not like people just stop using TurboTax because they’ve been doing their taxes for years.

Writing Great Process Notes: Some Tips

The key to writing great process notes is this: write down every step such that someone who is not you could follow them and successfully complete the procedure you are writing about. Even when you write notes only for yourself, you do not stay the same person year after year. An additional tip is to write process notes as if you are writing them for someone who has only baseline background knowledge, such as someone who is completely new to your research area. In this way, you ensure your notes are usable by anyone who might join your research project in the future.

When you use someone else’s tutorial to complete the steps, then make sure you add a link to the tutorial in your notes. That way, if you revisit the note and don’t remember a step, you can always return to the original source. I link back to the original sources in both of my process example above. However, a risk is that the tutorial or information page will eventually disappear, which has happened to me before. I recommend recording all of the important steps directly in your note in addition to the link. Sometimes I will paste steps directly from a tutorial page into my notes, such as for cooking recipes (not research, I know, but still useful!).

This goes without saying hopefully but write the steps in the order in which they should be performed, ideally using a bulleted list, or at least headers saying “step 1”, “step 2”, and so on. You see in my SciDB installation note that I use numbered lists to track steps. If order doesn’t matter, then mention this in the note.

Another tip is to practice searching your own notes before searching the web. The next time you go to look something up using your favorite search engine, just see what happens when you execute that search in your note taking app. For procedures you regularly perform, if you can’t find the answers in your own notes, then you should probably write a new one or update existing notes. Or if the answer changes and your notes go out of date, then you need to update them so they stay relevant. Developing a regular practice of using and reusing your own notes should help with note maintenance.

Writing Ideas Notes: an Example

Unlike my process notes, my ideas notes are pretty unstructured. Sometimes the ideas notes are just one line, like in this example:

An example of an ideas note. This idea eventually became one of the major research contributions for a conference paper that I published in 2019.

But these days I try to write ideas notes as self-contained thoughts, where I include the motivation, context, and if relevant the original inspiration for the idea, for example if a certain conversation or paper led to the idea. I prefer to write one note per idea, but this is not a strict rule. Here’s another example, which I originally wrote back in 2016:

An example of one of my ideas notes. This note mentions the system I built for my thesis, and some research questions of potential interest to the human-computer interaction and visualization communities. This note eventually became a research project that was also published as a separate conference paper in 2019.

I was at a conference presenting some work I did during a research internship the previous summer, and I was having lunch with my intern mentor. I was lamenting how I thought I couldn’t write a paper on my thesis work that the HCI or visualization communities would care about. My mentor pushed me to brainstorm ideas that were related to my thesis work and was kind enough to share some of his own ideas during the lunch, and I wrote down the best idea that came from our discussion. As it turns out, the idea recorded here eventually became a published paper three years later. The published project would have never happened without that initial discussion, but likewise the resulting project idea would have never come to fruition if it wasn’t remembered afterward (by me or Evernote).

Writing Great Ideas Notes: Some Tips

With ideas notes, the most important thing is to write down the idea as soon as possible so you don’t forget it. Add as many details as you have time for, but make sure you write every idea down, even the bad ones. If you are brainstorming and come up with multiple ideas, then feel free to list them in the same note. Here’s an example list from when I was brainstorming domain names for my blog site:

One of my ideas notes. This note shows many of the ideas I brainstormed for the Bits in Bites website name.

The list was so long that I struggled to get the entire note to fit into a single image! The name Bits in Bites doesn’t appear until near the bottom of the list, which is unfortunately off-screen in the image. As you can see, I came up with a lot of bad ideas 🙂 But what is key in these examples is that I didn’t limit myself when creating my ideas notes. Write as much as you can while the context is still fresh. Give your inner editor a break so your inner creative can shine through and generate lots of ideas and lots of details for those ideas, regardless of quality.

Writing Reference Notes: an Example

Reference notes are probably the most commonly written note in computer science research. You find an interesting bit of information and you want to save it for later, so you write a short note about it. I generally keep them fairly simple. I write a descriptive title about what the resource is, and then add a link to the original source. Here are some examples of reference notes I’ve written in the past:

I also keep reference notes for logistical things, such as my National Science Foundation (NSF) ID for submitting grant proposals, a link to the brand and logo information for my university, or a short description of my dietary restrictions for food orders for easy access.

Writing Great Reference Notes: Some Tips

Honestly, I don’t write a lot of reference notes. I am selective in what reference information I include in my notes. Why? Because reference notes are generally not connected to any specific research idea, process, or project, so they tend to be under-connected and therefore underutilized within my own information system. My general rule of thumb is to only add a reference note for content you have already had to look up multiple times. By the second time, you know that you have needed this information twice, and thus may need it again in the future. Here are some examples:

  • Professors in computer science periodically submit grant proposals to the NSF to raise funding for their research labs, myself included, so keeping a reference note on hand about one’s NSF submission ID makes sense.
  • My lab runs a lot of user studies, which we use to collect data to answer specific questions about human analysis behavior. We often run multiple statistical tests on the collected study data to determine the statistical significance of our findings. When you run multiple statistical tests over a dataset and measure significance using p-values, it is good practice to adjust the p-values based on how many times you reused the same dataset to conduct the tests, hence the reference above to Bonferroni correction.
  • I regularly present my work to other research labs and research groups, who generally ask for information about my presentation so they can advertise it within their organization. I often give the same presentation many times, so I keep reference information on hand that I can paste into an email or google doc for sharing purposes.
  • When attending a conference, daylong retreat, networking event, and so on, food may ordered for attendees. I have strict dietary restrictions so it is nice to have an existing explanation on hand that I can just copy and paste into a registration form or email.
  • When I read books, I like to save quotes about data, science, and knowledge. The last note in the gallery above is a snapshot of some of my favorite quotes so far.

However, there are some exceptions to this rule, since in academic research you never know when information will actually prove useful for a project. My typical exceptions are notes that I write when I learn from other researchers, such as when attending colloquium talks at my university, attending talks or chatting with fellow researchers at a conference, or writing notes on a paper I recently read. The third example above is a reference note for a paper I read on using GOMS models, a certain type of data-driven psychological model [2], to analyze website usability for people with visual impairments.

But again, these notes rarely connect to any particular idea or project in my information system, and as a result just end up floating around among my other notes with no established connections. For this reason, I try to only write reference notes for content I am likely to reference again in the future.

Writing Results Notes: an Example

Results notes are the most important note type in my information system. Basically any activity that stimulates my thinking on a particular research project or research idea I write down as a results note. For example, I use results notes to capture what I have learned from writing code, analyzing experiment results, and reading related papers for a given research project. Here are some examples:

As you can see, my results notes tend to be text heavy. They generally include a synthesis of my analysis findings, followed by my reasoning for why these findings are significant or interesting from a research perspective. The analysis findings themselves may be in the form of a visualization, such as in the first example, or even copy-pasted command line output, as in the fourth example. However, research is not relegated solely to running experiments and writing them up. In fact, a significant fraction of my research involves simply writing down my ideas and finding related research to bolster them. In the second results note example, I mention a paper I read at the time, and how the paper’s perspective on AI is interesting for visualization research as well. The third example is a snippet of an old draft of my doctoral dissertation. I often draft initial paper text in Evernote, then paste that text into a separate LaTeX editor to produce a shareable LaTeX project. This way, my paper text can stay close to my notes while I am still playing with nascent ideas, reducing context switching between applications. Later, when the ideas have matured more, then I may edit directly in a separate LaTeX editor, such as Overleaf or TexShop.

Writing Great Results Notes: Some Tips

I break results notes into two types: results from experiments, and results from thinking about my or others’ ideas. Both types are with respect to my current research project. I’ve written out separate steps that I recommend for each type below.

For experiments:

  1. Explain the motivations and goals behind conducting the experiment at the top.
  2. Describe your experiment as if someone will need to replicate it using your notes.
    1. If your experiments involve programming code, then add lots of comments to your code and include a detailed file explaining how to run it.
    2. If possible, use virtual environments to setup the code, that way you can avoid most installation snafus in scenarios where you have to run the experiment on multiple or different computers.
  3. Write a summary of the analysis findings, so you don’t have to interpret the raw data directly in your notes.
  4. Include a reference to the raw data so you know where to find it. If it’s small enough, paste the raw data directly in a separate note and add an internal link to the results note.
  5. If performing this analysis for a paper, summarize your ideas into a concise paragraph or two that can be pasted into your paper.

For developing research ideas using existing sources:

  • Explain the motivations and goals behind the analysis at the top.
  • Describe the key sources that inform the current ideas and arguments. Include full citations, and even include quotes to ensure the source ideas and attributions are clear.
  • Include links to PDFs of the key sources, for easy access later on.
  • Write your own ideas and arguments in more detail, citing the key sources as needed.
  • If performing this analysis for a paper, summarize your ideas into a concise paragraph or two that can be pasted into your paper.

Getting Started: A Template

To help everyone get started, I created a structured template for writing great ideas notes. The template is available here. A handy summary of the different note types is also available in the infographic I shared above (also available on pinterest).


My philosophy is that my brain will work better if I don’t have to memorize as much of my work. My brain is like a room, I can make the most of its space only if I keep it uncluttered. To this end, I offload the memory burden from my brain by writing a lot of notes as part of my research and even my daily life. However, it is not enough simply to dump my thoughts into random documents. Imagine what the library would be like if books were haphazardly placed on shelves, and if even the content within a book was random from one page to the next. No one would find the library particularly useful and would probably avoid going there, except perhaps to amuse themselves. The same goes for my notes. I try to keep my notes organized and detailed, so I know exactly what to look for and where to look when I need it.

In this post, I share four kinds of notes that I write as part of my daily work: ideas, processes, references, and results. I provide examples of each type of note from my own database of notes in Evernote, and practical tips for making the most of each type of note. In my next post, I’ll explain how I organize these notes into a powerful information network to boost my research productivity.


[1] Card, S.K., Moran, T.P. and Newell, A., 2018. The psychology of human-computer interaction. Crc Press.

[2] Newport, C., 2019. Digital minimalism: Choosing a focused life in a noisy world. Penguin.

Which Note Taking App Should I Use For My Research?

I have tried many note taking strategies over the years, from writing notes in a .txt file to writing notes in paper notebooks to writing notes using printable PDF templates to a variety of desktop and mobile apps, including Evernote, OneNote, and Color Note. Out of all of these options, I found that Evernote works the best for me. But how did I navigate this process? What were the main factors that influenced my decision? In this post, I will walk through these different options, and share my perspective on how to choose a note taking application that best suits your needs.

Paper Versus Digital Notebooks

I actually love to write things down on paper. Writing on paper helps me crystallize my thoughts and look for big picture patterns. Every morning, Monday through Friday, I write in my journal. When I’m working on a difficult research problem, I’ll often take out a sheet of paper and start drawing diagrams or writing bulleted lists. When I want to brainstorm new research ideas, I will write them on paper or on a white board. I occasionally write my tasks for the day on sticky notes. There is something satisfying and fulfilling about paper notes that I miss out on with digital notes. But as I already mentioned, my primary note taking system is not on paper, it’s in Evernote. How did I make this decision?

My main consideration when thinking about using paper versus a note taking app is how easy it will be to find my notes long after I have written them. My memory is not great. I have a long history of losing things. For these reasons, I try to structure my life so I don’t have to worry about losing physical objects, including paper notes or a physical notebook. If I only need a note for a single day or less, then I will use paper because I prefer that writing experience. But if I will need that note for the long term, for example for a research paper or proposal submission, then I migrate that content to an app.

In Defense Of Paper Notebooks

However, humans have been taking paper notes for thousands of years. Most apps don’t even last ten years. So for many researchers, paper notebooks seem like a safer bet than note taking apps. On top of this, you probably have a better memory than me! I never used a structured system for tracking my paper notes. If you learn from my mistakes and put a tried and true note tracking system in place, then going the paper route could work just fine for you. One system I particularly like is the commonplace notebook. Keep in mind though that the medium is not the critical factor in whether you will write good research notes. The critical factor is whether you will take the extra steps to organize your notes to make sure you can find exactly what you need when you need it. If you want to learn more about how to organize your notes to boost your research, my next post is on how to write excellent research notes for computer science.

Here’s an example of what some of Evernote’s features look like. There is a search bar in the upper righthand corner to support text search across my notes. I can also search by tags, recent searches, and Evernote’s recommendations. An Evernote note can be seen behind the search menu, which is actually a draft of this post! There are some hyperlinks in green at the top of the note, and part of my todo list for finishing the post underneath.

Choosing a Note Taking Application

If you are like me and would find it easier to track notes digitally, then you have a lot of options. My favorite app for taking notes is Evernote, but I have also received recommendations from colleagues for Microsoft OneNote, Notion, and even GitHub to keep everything in one place. Students have mentioned using Apple’s iCloud Notes as well. Rather than focusing on any one app here, I will instead discuss what I look for in a note taking app, and you can decide which of these points matter to you and what you might like to add to the list.

My Non-Negotiable Features: Text Search, Syncing Across Devices, and Hyperlinks

One of the main ways I find relevant notes is through text search. It only takes a couple months for me to forget the exact names and/or phrases I put in my notes, so text search is an absolute must for me. Most note taking apps nowadays support text search though, so this should hopefully be a non-issue.

Another important feature for me is syncing across multiple devices. Most of my best ideas come to me at random times throughout the day, such as when I’m walking to and from work, doing chores, or even when I wake up in the morning. In most of these cases, I’m not at my laptop, but I still have my phone on hand, so I prefer to take notes on my phone. When I write notes on my phone, the last thing I want to do is write the note over again because the note isn’t synced with my laptop. A related feature I look for is easy sharing of notes with people who don’t use the app. As an example, Evernote makes it really easy to give people view-only access to notes through public links, and it’s easy to turn sharing of public links on and off for each individual note.

Aside from text search, the main way I find relevant notes is through hyperlinks. For example, when I start writing a new note as part of a larger project, I’ll add a list of links to older notes at the top of the new note. I also add a reverse hyperlink in each of the older notes for accessing the new note. That way, if I want to quickly review a relevant note within the same project, I can hop over to the relevant note through the hyperlink and back.

Other Useful Features: Image Embedding and File Attachments

Finally, I also look for note taking apps that support images and file attachments. Sometimes I draw a diagram or take a snapshot and want to hold onto it for the future, so I just paste it directly into the note I’m writing. With an embedded image, I can include it alongside existing text, add a caption, etc. However, the image quality may not be great for embedded images, so in some cases I will attach the original file so I maintain access to the original source.

An example of how I use embedded images in Evernote. Here is a note I created as part of my research, which I used to track how people share images of visualizations they want to create or modify on stackoverflow. My computer science speciality is data visualization. I study how people create and interact with visualizations as part of my research.

Free Versus Paid Subscriptions

I actually have a paid subscription with Evernote because I use it a LOT. However, my honest opinion is that you should use the free version of Evernote until you bump into one of the freemium limits. For me, that was the limit on the size of individual notes. In the beginning, I never did anything very fancy with my notes. I just wrote text. But eventually, it got to the point where I would add images and files to my notes, which is difficult to do with just 25MB available per note. So I started paying for it. I see that the free version also has a severe limit on the total upload size per month (60MB). If you use the freemium version, I highly recommend avoiding adding any images or files, since this will eat in to the 60MB. If you stick to just writing your own text in the beginning (which is what I did), then the free version should work for a long time.

Which Subscription Level Should I Choose?

Currently, there are two subscription levels, “Evernote Personal” for 7.99 USD per month and “Evernote Professional” for 9.99 USD per month. If you want to pay for Evernote, here are some things to consider. I do not use most of the fancy features Evernote advertises. There are really only four features I take advantage of in the paid version (I’ll use Evernote Personal as an example): syncing unlimited devices, 200MB maximum note size, creating custom templates, and offline access on mobile and desktop. Technically Evernote shows me text extracted from images, docs, and PDFs when I search for things, but that doesn’t matter to me because there’s usually enough text in the note already to execute a successful search even without those extra files. And unless you upload lots of space-heavy files, such as high resolution images and video files, you are not going to bump into the 10GB monthly uploads limit. So you might pay for a lot of things you don’t need with the paid versions. That being said, the freemium limits are really just for writing text notes, and I want to do more than that. Also, I have a work laptop, personal laptop, and a smart phone, and I use Evernote daily on all three devices. The few features I do use are critical for my daily work, so I pay for them.

A snapshot of the information page for Evernote’s subscription levels. Evernote offers three levels: free, personal, and professional. I am currently a paying Evernote subscriber, but I used the free version of Evernote for years before I started paying for it. I use some but not all of the features in personal.

When to Buy a Subscription

Unless you are running your own business, I recommend just getting Evernote Personal. I already use only a subset of what the Personal subscription provides, and I would consider myself a heavy Evernote user. But don’t pay until you start getting frustrated with the free version. There is no sense in paying for something you may not use or even like. Try your desired app out first and if you like it then make a commitment with your money. Once you are ready to pay for a subscription, I recommend paying annually. Most subscription services will give you a modest discount if you pay annually.

Also, keep in mind that the specific app you use doesn’t matter in terms of writing useful notes. You can even use paper notebooks if you want. But if you don’t know how to write good notes in the first place, then you will be unhappy with your notes no matter what app or medium you use.

Choosing Which Devices to Use For Writing Research Notes

The next thing to do is to decide which devices you will use to take your notes. If you want to stick with free apps only, then my recommendation is to take notes mainly on your laptop/desktop computer, followed by a smart phone. I’m making assumptions here about what devices you have access to, but if you are a computer science researcher then I’m pretty sure you have a computer separate from your phone. Why no tablets you ask? Well, the free version of Evernote only allows syncing across two devices. Your main work computer and your phone should be the two devices, since you likely spend more time on your work computer at work and more time on your phone outside work. If you use a tablet way more than your actual work computer, then go ahead and install Evernote on it. Otherwise, don’t do it! You’re just giving yourself unnecessary headaches in the future having to swap Evernote between devices.


Whether you use a paper notebook or a digital one, you can write great research notes. The key is making sure that your chosen strategy includes all of the features you need for optimal note taking. Everyone’s needs are different, but I prefer to use note taking apps. I look for the following features in my preferred apps: text search, syncing across multiple devices, easy sharing, hyperlinks between notes, and support for embedding images and attaching files. Evernote is my favorite, and I have been a paying subscriber since 2017. However, definitely use the free version of your preferred note taking app until you bump into one of the freemium limits. No sense spending money unless you know for sure it makes sense!