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As a PhD student I generate a lot of pages with calculations, ideas and lecture notes.

Most of them are useful only for a short amount of time, but some may be important for much longer (when writing a paper, or when having new ideas to continue a once abandoned project). Typically I work on a few project simultaneously.

The question is, what is a good practice of taking and keeping notes? (With or without computer apps.)

Writing on single sheets (even if adding date and title) makes it easy to organize by topic, but also easy to loose. Keeping in one notepad makes it harder to collect useful things of one topic in one place.

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You should keep a research notebook, regardless of whatever other system you have for notes. The format of the notebook is up to you; it can even be public (see Carl Boettiger's as an example of an electronic lab notebook).

If you choose the pen-and-paper route for your research notes, and want to have the added flexibility/security of taking your notes with you (and also because it's good practice to do so), you should consider getting a scanner and making regular backups. You can then import these into a product like Evernote, Onenote, Circus Ponies Notebook, or MacJournal.

If you are using LaTeX, your options are somewhat limited, as most of the major tools for notebooking really don't support "live" LaTeX. Then you'd be better off using something like Aquamacs as a holder for your "notebooks" (LaTeX documents), and then using one of the above packages (or something like Papers or Paperless to organize the resulting PDFs.

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cough LyX cough –  badp Feb 15 '12 at 17:46
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@badp: LyX is not a "notebooking" program; moreover, I don't find the OS X implementation (which the OP would be running) to be all that good. Your mileage may vary, however. –  aeismail Feb 15 '12 at 21:45
    
Well it's as close as "live LaTeX" as it gets currently. I dunno about OSX but I've found out LyX is satisfactory for taking lecture notes (...that means notes during others' lectures right?) even when they involve a lot of maths. –  badp Feb 15 '12 at 22:38
    
As an alternative to a scanner, Livescribe paper notebooks and smartpen (livescribe.com) are a nice option - my lab uses those. It basically scans as you write, plus allows voice note recording and does handwriting recognition. –  weronika Apr 22 '12 at 15:38
    
@weronika: Thanks for the tip. –  aeismail Apr 22 '12 at 15:55
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I would definitely recommend a research notebook.

There are several different ways you can go about it.

  • The old school method of just using a paper notebook, where you enter data and computations sequentially by date. One is often encouraged to start a new page if one is moving to a new topic (and label the topic at the top of the page); but another possibility is to make use of the margins for noting the topic at hand.
  • An electronic notebook would be more searchable. On the other end of the spectrum from a paper notebook is a lab wiki. Some universities even have a university-wide Wiki platform available (for example, here's EPFL's wiki portal). In those cases you won't have to worry about administration issues, and many of those services are regularly backed up, and come with access control system so that you can limit your lab notebook to be only viewable by those in your research group.
  • An intermediate method is to just keep a private electronic notebook. I use a customised document class that I wrote for this specific purpose. If you use a good indexing package in LaTeX and make the effort to keep good indices, such a notebook can be very easily searchable. It also has the advantage that when preparing lecture notes or papers for submission, you can just copy and paste directly from your notebook.

If you prefer not to have a single notebook, what you'd need then is a sophisticated document managing system. For paper documents this will generally involve a filing cabinet, folders, and sticky labels. For electronic documents (say you digitize all your notes either by typing them up or scanning them), a lot of the citation managers, especially those that support multiple databases, can easily be co-opted for organising notes. On the even fancier side, you may want to use some sort of mind-mapping software.

Another option if you do not mind "showing how the sausage is made" is to follow the initiative of the Open Science Project and blog about your research as you go along.

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+1 for mentionning Mind-Mapping software. Usually you can use "tab" or "ins" to create subnodes, "return" to create a node underneath (and at the same level than) the current node, and you can move a node+subnodes using "ctrl+keys" (to move up/down/sideways in the hierarchy). It makes organising thoughts on the spot (or later) very effective (+ force you to decide how to organize them). –  Olivier Dulac Nov 5 '13 at 12:00
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For some pretty well-thought suggestions about organizing your notes (without being specific to any application, and dealing with both electronic and paper notes), you can refer to this link.

A summary of what methods are discussed:

  • Keeping Track of Information Online: How to organize your notes in a sensible directory structure on your computer.
  • Version Control: Using the power of SCS packages (Mercurial happens to be my favorite due to its ease of use) to store multiple revisions of your notes.
  • Keeping Track of Paper: Finally, how to keep your office clutter-free.

Bear in mind that the link is a bit dated, so it doesn't refer to online services like Google Docs which can be effectively used to keep a back-up of your notes online!

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across the StackExchange, single-link answers are strongly discouraged. Please could you summarise what's on that link? The idea is, AIUI, to build up great answer content here, not to just link to good answers elsewhere –  EnergyNumbers Feb 15 '12 at 11:43
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OK - a summary coming up! Let me know how to improve it if you don't like it... –  TCSGrad Feb 15 '12 at 11:45
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I like to keep the paper option, since most initial ideas are usually a waste of time to typeset using LaTeX or any other computer system. I really hope that does not sound like advertising, but I find the combination of Atoma notebooks (picture below) and sticker tabs quite efficient. You don't lose sheets, and you reorganise them as you wish, as many times as you wish.

enter image description here

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If you have Microsoft Windows Office 2010, I would recommend OneNote as a really handy way of tracking your notes, images, miscellaneous ideas etc.

For a non-MS cross-platform app, you can try Evernote - it is similar to OneNote, with the added advantage of syncing your notes over multiple computers/tablets etc.

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Actually I use Evernote, but it does not support neither LaTeX nor interlinks between notes (so I use it only for random notes, much less as a research notebook). (I am on MacOSX, BTW.) –  Piotr Migdal Feb 15 '12 at 10:48
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Part of my answer in this question applies here as well; when reading papers, I've found it useful to write down notes on paper, and then put the notes in a 3-ring binder, along with the paper itself. A similar technique can be used electronically using either Papers or Evernote... take notes on each paper and attach the notes to the paper (or the to paper if using Evernote). Personally, I found it much better to take notes by hand, as you can scribble in margins, write equations, draw out plots, MUCH faster than if done by hand.

I've also made it a point to keep all notes from classes I took. I've found numerous instances where I referred to notes from a course I took a while back. It's much easier to re-read your own notes (assuming you take good notes) than to learn it from a book where you're unfamiliar with the layout and presentation style.

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I find that using Endnote (or a similar reference software) kills two birds with one stone. I find typing up references correctly very very tedious, but absolutely essential. You can import a lot of the references from databases (less typing needed) and then add your own notes, keeping it all in one place. You can add files or scan your paper notes or photos. It is also easily searchable. Plus when it comes to collating your reference list or bibliography, it automatically inserts and formats the articles in the style you selected. That alone can save days when finalising papers.

Endnote works on both macs and pcs and also has an online version. http://www.endnote.com/

I also found that universities usually buy a site licence for Endnote or another similar reference software that both staff and students can use for free.

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The question is about own notes, not references. And putting tones of references and own notes in one place is a suicide. –  Piotr Migdal Feb 22 '12 at 11:03
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I find that a mix of both worlds (physical and digital) works best for me. People have different ways of retaining and processing information.

Productivity apps are quickly becoming a popular and efficient choice in managing note, documents and other information. You may want to try applications like Evernote, Dropbox or Google Drive or a mixture of the three.

Also recognizing this growing problem of information overload and how to address it, there are many new and improved data capture applications that cater to the myriad of problems stemming from the need to organize information efficiently while making it accessible no matter the age of the info. You may want to try new apps around like Doo or Phoenary to enhance your note-organizing and information capture.

Hope that helps!

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