I reached the point in a thesis project where my notes were becoming harder to manage than the actual writing. I had articles, quotes, half-written ideas, and possible section headings scattered across different places, and I needed a better way to see how everything connected.

That’s when I started paying more attention to outlining software. I like being able to move sections around before committing them to a finished document. It feels much easier to change the structure when the ideas are still in an outline than after several pages of prose have already been written.

I’ve also been experimenting with a combination of tools rather than expecting one application to handle everything. Zotero works well for keeping research and references together, while Grammarly is useful later when I’m cleaning up sentences. For the actual structure, though, an outliner seems to solve a different problem.

I’ve also looked at different resources related to thesis writing, including the thesis writing material on CollegeEssay.org. I’m less interested in using any one resource as a complete solution and more interested in seeing how different people approach the transition from research notes to a structured paper.

The biggest question for me is where the boundary should be between outlining and drafting. Sometimes I find myself writing full paragraphs inside an outline because the idea is fresh, but then I wonder whether I’m making the outline too detailed.

I’ve tried both approaches. A very short outline gives me freedom while drafting, but I can lose track of the larger structure. A detailed outline gives me a clearer path, although it can start to feel like I’m writing the paper twice.

For longer projects, I’m beginning to think the useful part of an outliner is not simply creating a list of headings. It’s being able to test the structure, move ideas around, identify gaps, and see whether the argument actually develops in a sensible order before spending too much time polishing the prose.

I’d be interested in hearing how others here handle this. Do you keep your research structure separate from your writing outline, or do you combine the two? And at what point do you stop outlining and move into the actual draft?

Thanks for sharing your process with us. I haven’t used outlines for writing in a while, so take my comments with a grain of salt. But I don’t think you should worry too much about how much or how little you add to your outline. Whatever you need is the right amount. With a lot of outliners, you can add a note to a node (or topic), which you can view or not view. That way you capture the thought you don’t want to lose, but can hide that text to keep the outline looking manageable.

I think an outline benefits a lot from a notes database. Obsidian would be great for that. It would be nice to have outline topics linked to tags or some other grouping of notes that pertain to the topic, but I've starting thinking it's not necessary. Use the notes database as a reference answering the need of the moment.

Detailed outlines kill stories for me, so broad strokes in the outline, detail about facts in the notes database, and narrative in the manuscript. At this point in my yet-to-be-productive writing career, that makes sense.

It also seems to me that the outline isn't set in stone. If an idea comes to mind that isn't in the outline, don't automatically flesh it out in the manuscript. Instead, update the outline. You can catch up in rewrites. I've found this keeps me from brain dumping.

Good luck. It would be awesome to hear the evolution of your writing and planning style.

As a fellow academic/researcher, I can relate to the issue you have with notes and all things related to research scattered in various folders and in various apps.

For the actual writing up of a paper, using a binder system (see Scrivener) helps me, as it works very much like an outline for longer texts (aka long-form writing).

But this still didn't solve the problem I had with different notes in different folders and apps. When working on a section of a paper, I would remember that I had worked on an idea, but I was at a loss as to which app or folder I filed the idea in. I lost many an idea because of this issue. These ideas and thoughts were made at a time when I couldn't foresee what they would be useful for. It is only through the process of writing that I can see the connections between ideas. Ideas that I had formed even years before.

I use a Mac and initially tried the app Hookmark, but the system ended up breaking down. Along came Obsidian, which worked for a while, until the plugins I used stopped working. Other PKM apps started to appear that solved the issue I had with broken third-party plugins, but they didn't have the binder system in the way I needed to outline and write a paper.

So basically, I was stuck having to work with a few different apps, trying to work out which one was the absolute best tool for a specific task, and using them so much that they had become muscle memory. At least I was finally able to get the number of apps down. I also developed a basic hierarchical folder system, which, for the most part, worked for me as I was able to locate certain files quickly. I loaded this folder system on a cloud folder and backed it up on the Macs I have. I wasn't fully satisfied with the system that I had developed. Far from it. But it was the only system I had that somewhat worked. The critical problem I had was that I couldn't pinpoint what exactly I needed because I didn't really know what I needed.

I then stumbled across the app MojoPad https://mojopad.app in this forum. @macosxguru wrote a wonderful blog post about the app (https://bicycleforyourmind.com/mojopad-is-a-wicked-wiki that had me excited. I downloaded MojoPad and played with it for a few days, and really liked what I saw. I decided the best way to put the app to the test was to use it for actually writing up a paper. I found the app needed a little fine-tuning and reached out to the developer. The developer, Mark, was very responsive and incorporated my needs, often overnight. MojoPad can be very overwhelming at the start. There are so many features. But because the manual is itself a Wiki database, I was quickly able to work out how to tailor the app to work for me. I would try out any new features on the manual itself.

Now MojoPad works brilliantly for me. It solves the problems I was having all these years. I realised that what I needed was an app that had a binder system COMBINED with a database. I could search and find notes in the database that I needed for the paper I was writing, AND I was able to actually write the paper side-by-side in MojoPad.

Further, I was able to file away in the database new ideas I gained in the process of writing the paper, but was more appropriate for another paper. I can also see myself revisiting some of the same old notes and applying them in a different way in future papers or different research projects. In addition, I often come across other features that I first thought would be of no use to me, but ended up being really, really helpful. Like the text-to-speech feature and even create audiobooks! For important papers I come across and need to properly absorb, I export them as audiobook files and listen to them in bed. Listening to papers in this way had helped me come up with breakthrough ideas I would have never come across by reading alone.

You can shape MojoPad to work the way you want it to. I am very frustrated with apps that force you to work in a certain way. MojoPad is, for the most part, very flexible.

I know this must sound like a paid advert. It is not. I paid for the app. I am just deeply grateful that a talented developer was able to create a tool that helps me do my work so that I, in turn, can make my small contribution to make that world a little better. I am also most thankful to this forum for the enthusiasm that the members have for sharing information about apps like MojoPad, along with their varied opinions and takes. ;)

Can MojoPad be further improved? Definitely. And I am sure the app will continue to be improved. I wish there were an iOS version of the app. But then again, I don't really see myself using all the features of MojoPad while on my iPad or iPhone. But I would like to be able to access the database and work on certain notes when I don't have my MacBook Air with me or am seated in front of the desktop setup. I had situations where inspiration struck in the strangest of places, like in my doctor's waiting room. Maybe there will be a way for this to happen with further development.

If you are Window's or Linux user, there is good news for you. According to Mark's post in the MojoPad forums, both versions are scheduled for release sometime next month, in October.

I wish you all the success in your thesis write-up. Many folks don't realize just how hard and stressful writing a thesis can be. But you will be glad that you stuck with it. Writing the thesis gives you the skills to work on research independently. It is truly a passage of membership to the academic community. If you are in the final stages of writing up, I would steer clear of trying new software. Just concentrate on writing and make sure you back up all your work, and create another backup! Cheers! :)

Elias Denver wrote:

I reached the point in a thesis project where my notes were becoming harder to manage than the actual writing. I had articles, quotes, half-written ideas, and possible section headings scattered across different places, and I needed a better way to see how everything connected.

Elias Denver wrote:

I had articles, quotes, half-written ideas, and possible section headings scattered across different places, and I needed a better way to see how everything connected. That’s when I started paying more attention to outlining software. I like being able to move sections around.

I can move sections around almost as easily in Ulysses as I can in my outliner. But for me, the outliner serves best as a detailed map of the work, rather than as a pile of research or the primary space for drafting. I use and refer to all three simultaneously, which can mean three apps plus a web browser.

The biggest question for me is where the boundary should be between outlining and drafting. Sometimes I find myself writing full paragraphs inside an outline because the idea is fresh, but then I wonder whether I’m making the outline too detailed.

I don’t discriminate between the two. I’ll write in an outline (hundreds of pages is not unheard of) but when I want a more comprehensive overview, I’ll collapse a longer block of text and have a higher-level parent node summarize what it contains. I’ll often make a sister node containing metadata or discussion about the draft material. When I’m 'seriously' drafting,I’ll copy/paste or rewrite material from the outline into Ulysses. But as long as my outliner is fast and can handle large amounts of text well I’ll write in it rather than switch to another app. There’s no hard-and-fast rule.

A very short outline gives me freedom while drafting, but I can lose track of the larger structure. A detailed outline gives me a clearer path, although it can start to feel like I’m writing the paper twice.

Writing is rewriting. It doesn’t bother me to rewrite something from one app into another if I was going to rewrite it within a single app anyway.

Do you keep your research structure separate from your writing outline, or do you combine the two? And at what point do you stop outlining and move into the actual draft?

Outlines are essential to the research structure, are part of the writing process, and form the bones of the final writing. I outline and draft and I don’t draw a hard line between them. The outline informs the draft structure while also containing thoughts about alternative structures and notes on approaches I’ve tried that didn’t work. (I just put that material in sister nodes to the draft.) I just checked an OmniOutliner page I’m working on that contains research notes and ideas. It’s maybe three pages with all the children collapsed, but ~130 pages expanded and printed.

I've been combining Obsidian-Wiki, which allows an LLM (like Claude) to read and manage an Obsidian vault for you, with Zotero MCP, which allows the LLM to read and interact with your Zotero database, including your notes. I've found it to be a very powerful combination: it takes your own reading annotations and turns them into a living, growing, wiki that you can talk to. It improves and gets better the more you use it. I instruct it to always cite its claims from my own Zotero DB, so I can check that it isn't hallucinating when I use something it says. For instance, I am researching educational policy, and it was able to go through my notes and make a policy timeline for me that has been very useful during the writing process.

https://github.com/Ar9av/obsidian-wiki

https://stevenyuyy.com/zotero-mcp/