Recommendations for Organizing Research Notes

I recommend Tomboy, which is a desktop note-taking app for Linux, Windows, and Mac OS. The features that I like are:

• Different notes can be linked via a WikiWiki system: so I can reference ideas from different projects
• Math can be displayed online by installing a LaTeX plug-in.
• Links to webpages and files in the filesystem can be automatically created and opened with one click: so I can quickly access things outside of the note-taking app, such as experimental result text files.
• Basic formatting (bullet lists, highlighting): unfortunately tables are not available, I think
• Search function: so I can quickly pull-up old notes

Overall, I think Tomboy is a light-weight solution that answers most of my needs. The one thing it doesn't do well, though, is bibliography management. For that I use a separate app, JabRef.

For notes about papers I read, I use Zotero. There you can keep references to all papers you're interested in, and they're immediately available on any computer you use. When you see a paper on citeseer or the ACL Anthology you can click a Firefox button, and it extracts the information and puts it in your Zotero database. Then you can add notes there. When you write a paper you can drag and drop references from Zotero, and they will be added in your paper (e.g. as bibtex snippet).

If you're worried about lock-in (of your notes etc.) into this specific system -- Zotero can export its whole database as a big BibTeX file, including the notes you added.

(For other research notes, see my other answer.)

It may sound funny, but I just use Gmail, and it works great for me:

Whenever I have an idea or get some specific result or run some long command that's hard to remember I write or paste it into an e-mail that I write to myself.

I write to [email protected]. This +research is not part of my normal [email protected] e-mail address, but Gmail allows these extra specifiers, and I have set up a Gmail filter that automatically labels such e-mails with "research", so I can find and look at them all easily.

Altogether, these labeled e-mails are like a research journal. Everything is chronologically sorted and easily searchable. And I can label them with additional labels, star them etc. Plus, I'm in gmail all day anyway, so this is the natural place to have these notes for me, and they will be available on any computer I use.

Whenever I have additional comments on an earlier note I just "reply" to it, creating a thread that's always displayed together.

Also, Gmail has (limited) HTML capabilities, which I sometimes use in these notes, to put commands in Courier font or use bold or italics. Latex math capabilities would be nice though.

Sometimes I have longer derivations etc. that I do on paper. I then scan the paper and send it as PDF to ... you guessed it. Due to the subject line and maybe some keywords that I add in the body of that e-mail I can easily find it again later.

I use MediaWiki to make notes. If you have a web server (or a space on a shared server), you can make notes on MediaWiki when you are in any place. Privacy is not a problem, because it has an ACL system.

MediaWiki supports categories. It also supports Latex.

Moreover, MediaWiki has a very strong template system. Basically, you can get any function based on that, if you can do programming.

I like the low-tech solution -- keep one notepad for scribbles and another one for good notes. When I get some derivation or formula I like to remember, I just copy it by hand from the first notepad into the second one. Then when the good notepad gets filled with enough interesting things, I do a summary of interesting results as a latex document.

For notes on specific research papers, Mendeley Desktop works well for me. You can either add free-form notes, which are instantly searchable, or insert notes and highlights directly into the PDF. If necessary the PDF can be exported with annotations. The major upside is having all paper PDFs and corresponding notes within the same context. With the added option of exporting references directly to MS Word via the Word plugin, I'm pretty much a happy camper.

There are some obvious lock-in issues, but apparently all data is available in a local SQLite database. EndNote, RIS and BibTex export is also supported.

For general notes, Evernote works fairly well although the Desktop client seems to get slower the more data you add. The automated OCR is pretty impressive, though. I'm using Nozbe for project management, and I like the way it does tag-based integration with Evernote.

Notes written in plain text files will still be usable no matter what computing system one uses. I strongly recommend avoiding lock-in to any particular program and just using plain text.

I currently write my notes in org-mode, which in an Emacs outline editor that supports inline Latex equations. Emacs is a great text editor and org-mode is a great outline editor. I name every file after its Bibtex key (if I'm making notes about a paper); otherwise I just choose an appropriate name. They all live in one directory and I use the OS full-text search or grep to find information quickly. I store my notes in a version control system. Currently this is Subversion but I'll be putting them on Github soon.

I've used google wave for this with some success. It's nice because it's a mixture of structured and unstructured, you can easily get other people to see/edit it, and there are many bots that give you latex support.

I also like keeping latex files related to the projects I'm working on, and just typing derivations/rationales there, and eventually trying to massage them into something useful.

xournal is a useful too especially when dealing with "untypable" stuff. Can be downloaded from here.