How to Organize PDFs and EPUBs for a Course or Thesis
One library, folders per course or chapter, and notes attached to the reading. Includes imports from Drive, Dropbox and Zotero.
The simplest way to organize PDFs and EPUBs is to put every reading in one library, sort it into one folder per course or thesis chapter, and keep your highlights, notes and bookmarks attached to the readings themselves. That way, finding the paper you need in week ten takes one click, not a search through Downloads, Drive, Dropbox and your email. This guide shows a system that works, and how to set it up in Nook.
Why Student Libraries Fall Apart
A normal semester produces files in at least five places:
- Papers downloaded from the library into Downloads
- Readings your professor posted as PDFs on the course site
- EPUBs of assigned books
- Files saved in Google Drive or Dropbox
- Papers in Zotero
Add a thesis and it gets worse. Within a month you have three copies of the same paper with different names, no memory of which one has your notes, and no idea which readings are done.
The problem is not discipline. It is that reading, marking up and filing live in different apps.
The System: One Library, Folders, and Notes on the Reading
1. One library. Everything you need to read goes into one place. In Nook, that is your library, where PDFs, EPUBs, Word files and web articles live together.
2. One folder per course or per thesis chapter. Keep it flat. A folder named for the course (or the chapter you are writing) is enough. Deep nesting makes things harder to find, not easier. Folders are part of Nook's new library: new accounts get it by default, and existing accounts can opt in.
3. Highlights and notes on the reading itself. Marks made in the reader stay attached to the paragraph they came from. You do not have to hunt through a separate notes app to remember what a highlight was for.
4. Bookmarks for what you will cite or review. Bookmark the paragraph you will need next week, such as the definition, the result or the quote.
5. Done is a state, not a feeling. Your reading progress is saved, so you can see what you have finished and where you stopped in the rest.
Getting Files In
You do not need to move everything by hand. Nook accepts almost any PDF, EPUB or Word file, and it connects to the places your files already live:
- Upload directly. PDF, EPUB or Word. Scanned files go through OCR on import.
- Google Drive. Connect with Google. Nook opens Drive's picker and downloads only the files you choose, not the rest of your Drive.
- Dropbox. Pick PDFs, EPUBs and Word files. Nook only sees the files you pick.
- Zotero. Import the research PDFs already stored in your library. See Zotero + Nook.
- Readwise Reader. Import saved articles together with their highlights and notes.
- Instapaper. Bring saved articles in to finish them.
- Notion. Import pages you share with Nook.
- The browser extension. Open any web page or a selection in Nook while you browse.
Imported files land in a folder for that source, such as Google Drive or Dropbox, and you can drag them into your own course folders.
A Setup for the Semester
Week 0: Create folders
Make one folder per course. For a thesis, make one per chapter, plus a Background folder and a Methods folder.
Week 1: Import
Bring in the syllabus readings that are already available. Do not wait to import until you are about to read. It is easier to import everything once and read from the library.
Each week: Read from the folder
Open the folder for this week and read in order. Use chunking or Autopace for the dense ones and a Pomodoro session to stay in the document.
While reading: Mark, note, bookmark
Highlight the main claim, attach a one-line note where you disagree or want to follow something up, and bookmark the passages you may cite.
After reading: Check with a summary
Open the Summaries panel to see the takeaways for the reading and check whether you caught them. Tap a point to jump to the passage it came from.
End of week: Review your notes
Spend ten minutes reviewing your notes and bookmarks for the week's folder. This is what makes the reading stick.
For a Thesis
A thesis library behaves differently from a course folder: it grows for a year, and you need to re-find things.
- Folder per chapter, plus Background and Methods folders.
- Bookmark the quotable paragraphs as you read, so the literature review writes itself from bookmarks.
- One note per paper with your three-sentence summary: what they asked, found and what it means for your thesis.
- Keep citations in Zotero. Nook is not a reference manager, so keep your bibliography there and use Nook for reading and thinking. See How to Read a Research Paper.
Set up your first folder and import this week's readings. The trial is 3 days with everything included, then $5/month or $39/year.
What Imports Well
- Works well: journal articles, research papers (including STEM papers with figures and equations), reading packs, reports, theses, monographs, EPUBs and plain-layout textbooks.
- Check before you rely on it: layout-heavy textbooks with callout boxes, sidebars and text in shaded panels. The boxed content can be lost in OCR. Use the EPUB if you have one. See can you study from a PDF textbook.
Frequently Asked Questions
What is the best way to organize PDFs for a course?
One library, one folder per course, and notes and highlights made in the reader so they stay attached to the reading. Import everything once and read from the folder.
How do I organize research papers for a thesis?
Use a folder per chapter, bookmark paragraphs you may cite, keep one summary note per paper, and keep citations in a reference manager such as Zotero.
Can I import files from Google Drive or Dropbox?
Yes. Nook connects to both. It only downloads the files you pick, and imported files appear in a folder for that source that you can drag into your own folders.
Can I use Nook for EPUBs and Word files too?
Yes. Nook accepts PDF, EPUB and Word files, and web articles, in the same library.
Does Nook replace a reference manager?
No. Use Zotero or a similar tool for citations and bibliographies, and Nook for reading, marking up and keeping your notes.
Related reading:
- Best PDF Reader for Studying: the apps compared
- Zotero + Nook: read the papers in your library
- How to Take Notes and Highlights While Reading on a Screen: a simple method
- How to Read a Research Paper (and Keep What You Find): the staged read
- How to Use Bionic Reading on PDFs: read dense files with less effort
- Best PDF Reader for ADHD: if focus is the problem