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I am a softie who (for the most part) writes Twitter threads when students and scholars of under-represented communities and countries of the Global South write to me. So, here's a by-request thread on how I organize my folders and some practices (not sure if they're best!)
Like anybody, I, too, get disorganized every so often. This is something that happens to me when I am overwhelmed and I just say "oh, I'll dump my files in my main Dropbox folder" and then I have to take an entire day to re-organize my life.

I use various cloud-based services.
In OneDrive, I have my "Main Research Library". I have folders for each and every topic of interest to me.

I try to make each folder name as descriptive as possible.
Dropbox has my core working archive.

Most of my work is here (though as you can see, my folders do not always "jive", like the "Pandemics and Biopolitics" one, because the group of researchers I am working with on this topic and I have not yet decided if we're writing anything.
You will notice I have a folder with "Vancouver Studies".

I've always wanted to write and publish a paper using my hometown as a case study. Sadly, a reviewer asked me to cut it from one of my papers so it'll have to wait yet another year. I do have a few projects on it.
My "My Papers" folder is organized by year. This is problematic, as you will find out, because some papers take YEARS to get published. So if you started it in 2017 and go it published in 2020, it becomes a problem (I'll explain to you how I deal with that in a minute).
This paper has already been accepted and is in press, so I don't feel bad about sharing the folder structure (it's for my forthcoming Journal of Environmental Policy and Planning paper)

Note how I make new folders every time I get an R&R
Now, the person who asked me for this Twitter thread asked me for suggestions for students, to help them organize their papers.

If I were to tell my students to organize their academic lives again, this is the structure I would recommend:
This is a refined version (all diagrams made with mindmaps.app/#)

To be clear: this is EXACTLY how I organized my files when I wrote my undergrad, Masters and Doctoral theses. My method has not changed even now that I am a professor.

(some call this a tree diagram)
I'm a Virgo, an "Upholder", a Type A and someone who thrives when having a clean and organized environment, both physically and mentally. I hope these suggestions will be useful to those who follow me.

</end thread>
One last item.

OF COURSE my root Dropbox folder gets disorganized. I have to finish 4 articles within the next 2 weeks so my root Dropbox looks like this right now.

Because I promised several followers that I would write a blog post on how to write research grant proposals...
This means that I need to spend some time creating a folder called "Grant Writing Books" and moving it to OneDrive.

But I seriously haven't even had the time to do that (I may just do that right now).

Some articles I've downloaded I want to read are there too.
And, like anybody else, I also have a "To Organize" folder where I dump stuff.

I set time aside every weekend to reorganize my files, but because I already have a system, it takes me SUBSTANTIALLY less time to do it nowadays.

</end thread, for realz>
Addendum:

Dr. Robert A. Karl @RAKarl has developed an amazing set of techniques to organize and process materials and files if you do archival work across different sites. This thread is gold if you're a comparativist, a historian or do archival work
NEW BLOG POST - Organizing work/school-related digital files raulpacheco.org/2020/07/organi…

This thread in handy blog post form, with additional text.
Missing some Tweet in this thread? You can try to force a refresh.

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