Note Taking and Note Organization

It’s important for a grad student, especially a PhD student, to keep track and organize his/her notes (in general, read papers with comments, project documents, on-going papers, ideas,…). There are several requirements:

  1. It should be easy to categorize and search your notes, ideally with tags or labels or keywords.
  2. It should be not difficult to include mathematical formulas and (infrequent) pictures/drawings/sketches in your notes.
  3. The notes should be long-lasting, i.e. you can easily store and organize them for several years. It should be easy to make back-ups.
  4. It should be easy to access the notes.
  5. It should be cheap, ideally free.

Several approaches could be thought of:

  • Using paper notes, organized by labels, kept in boxes or folders: satisfies #2, but doesn’t satisfy other requirements (well).
  • Using document files in your local computer: if LaTeX is used, it will be easy to type in mathematical formulas, however how to organize and search your notes (requirement #1) is a big question.
  • Using blogs or wikis: a modern approach which satisfies most requirements, except #2. Although there are plug-ins which allows LaTeX code in entries, they are often limited and require your own host (you usually cannot use these plug-ins on a free host).



  • Use open format, preferably text-based.
  • Support LaTeX in some way.
  • Portable: believe it or not, I am using three popular OS’s at the same time: Windows XP, MacOS Tiger, and Linux (Ubuntu). As a consequence, the software must be able to run on all those three platforms. This is also a reason why I prefer an open, text-based format to a binary format.

You can take a look at this page: just found a note management software for MacOS at However, the software is commercial ($29), not portable (only run on MacOS) and does not use an open file format. I think that writing a similar software in Python is not difficult, if only textual data is supported (LaTeX, simple text), not images (which can be embedded in LaTeX code), not Web-pages, not PDF’s. offers free blogging (which is much more professional than the Yahoo blogging system). Good news is that supports LaTeX mathematical typesetting. Bad news: though supports tagging, it doesn’t and won’t support tags searching (for example, search all entries that have tags “truong” and “love”, or list all current tags), it offers limited space for uploading files, and it doesn’t (and I think, won’t) support advanced typesetting features. I think will be useful for jotting down your brief ideas, or ideas that you want to be available to the public, or non-very-technical ideas.

Update: I finally found an ideal solution, at least for me: the org-mode in Emacs. It satisfies ALL my requirements. If you feel confident using Emacs, you should check out org-mode. Moreover, you can also implement a perfect GTD system using org-mode.

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