Wikify my math
December 25, 2008 7:22 PM   Subscribe

Should I be using a wiki to collect my notes on mathematical research? Which one?

I am a mathematician and I generate a lot of notes, thoughts, and computations. For many years, my method of gathering these was to write everything down under dated headings in a series of spiral notebooks, then index each notebook as it was finished. Drawback: my handwriting is really hard to read after a couple of years, and I often found it easier to work out something again from scratch than to try to follow the reasoning in my scribbled notes. Besides, since I work on a lot of projects at once, the notes relevant to project X might be scattered over various notebooks in hard-to-find ways.

For the last year or so, I've been LaTeXing short notes on various subjects; having a nice clean document makes it much easier to keep track of what I was trying to say, but now I have tons of .tex and .pdf documents on my hard drive and in order to find the one I want I often have to remember the filename -- or I just forget the document exists altogether.

It occured to me that the correct platform for what I really want to do might be some kind of a wiki, where the notes, .pdfs, links, etc. associated with a given project will stay "in one place," where I can easily link to or even include outside documents, and most importantly where I can easily locate all notes relevant to a given question.

Are any of you mathematicians or mathematical scientists who use a wiki in this way? Am I right to think this might be useful? And if so, which of the many options should I be thinking about? I'm a bit confused with Google Sites, PBWiki, Tiddlywiki, VoodooPad, instiki, and more all floating around offering what looks like substantially similar functions. Or should I just learn how to use Zotero or Google Desktop or Papers and tag the hell out of all my floating .pdfs?

Things I care about:

* Must be easy, really easy, to set up on a Mac. (i.e. presume I don't know how to use Linux.)
* The search functionality should be really good.
* Should be able to export well, since I'm not at my computer all the time and I do want to have easy access to printouts.
* (related to above) should be in a sufficiently stable format, or be sufficiently exportable, that I don't have to worry about a company going under and my notes being inaccessible; this is stuff I want to be sure I have access to years in the future.

Things I don't care about:

* Good TeX formatting; I don't mind writing notes "e-mail style" without the symbols.
* Whether it's hosted or sits on my hard drive -- though ideal, I think, would be something that was hosted but mirrored itself on my laptop so that I could work on it off-line.
* Privacy -- i.e. the thought of Google or whoever else having this data stored on their servers doesn't trouble me.

This old thread has some good suggestions, but it's two and a half years old and the criteria are somewhat different.
posted by escabeche to Computers & Internet (18 answers total) 11 users marked this as a favorite
Tiddly Wiki works pretty well. Set-up involves downloading and opening it. I haven't used the search function very much, everything I have is organized by tags. I'm pretty sure most of it is in HTML and that's not going anywhere anytime soon.
posted by 517 at 7:29 PM on December 25, 2008 [1 favorite]

I'd either use Google Docs (which has an offline mode, handy) or PBwiki.
posted by zippy at 7:49 PM on December 25, 2008

There are multiple wiki hosting sites -- seems to be popular -- and some of them allow you to lock reading away from anyone not logged in. I believe you retain all copyrights (so you're not giving away your thoughts) and bonus points for being accessible everywhere.
posted by dirtynumbangelboy at 7:49 PM on December 25, 2008

Before you mentioned you were on a mac I was going to suggest Microsoft OneNote. A product from Microsoft that is actually useful.

A Wiki could get rather annoying since you'll have to get into the habit of Wiki notation if you're not going to use the Rich Text editor that some of them have. In which case, Google Docs might be your best friend. Combine it with Google Notebook for some fun (which can export to Google Docs) if you're doing alot of stuff online.
posted by miasma at 8:58 PM on December 25, 2008

What about Evernote? You can use it offline and then synch it. You can download it to a usb and take it with you. It saves as you type. They say they have 500,000 users so far, makes me think they will last. But if they don't last you would still have your offline copy. Search is great.
posted by cda at 9:03 PM on December 25, 2008

I've used TiddlyWiki a couple of times and it has been pretty great. Backup shouldn't be a problem either, since the whole thing is just one html file. If you have a look around the web, there are a ton of tutorials on how to organize/use TiddlyWiki.
posted by pwicks at 9:15 PM on December 25, 2008

(not snark): I'd have thought that you already have a good solution, since you should be able to use Spotlight to search your notes. Can someone explain what using a wiki would add?
posted by lukemeister at 10:12 PM on December 25, 2008

From a question I asked here; I chose wikidot; its free; easy to use; private if required; requires no downloads yet lets you download your pages as backup.
So far I am happy.
posted by adamvasco at 2:07 AM on December 26, 2008

I use devon think pro on my mac
posted by compound eye at 4:21 AM on December 26, 2008

I am not a mathematician, but I have a similar need to organize research notes. I and other colleagues on the mac have been using Journler for this purpose. Journler is not a wiki, but I found Journler integrated better with my overall use of my computer compared to my previous attempt to use VoodooPad for organizing research notes.
posted by needled at 6:20 AM on December 26, 2008

The amount of work setting up and maintaining a wiki will be more than just being more careful about the naming and organization of your LaTeX stuffs.
posted by TypographicalError at 7:17 AM on December 26, 2008

Best answer: I've been trying to come up with a way to make a wiki work for research for a few years now, and have pretty much given up. My grand plan now is to spend the week after New Year's going through all of last year's notes, and making a master index document with hyperlinks to the others. I'm hoping that plus SpotLight will do the trick.

As far as wikis go, the ones that came closest for me were
1. TiddlyWiki, for all the reasons noted above (single HTML document, portable and backupable). Also, there are several modified versions, including one for scientific notes and TiddlyMath and one that claims to have LaTeX. It's lasted longer than I thought it would, so must meet some people's needs.
2. PmWiki. A nice balance, I think, between the barebones TiddlyWiki and the full-on MediaWiki. Uses flat files for storage, so you don't have to muck around with SQL. Under active development (though slow for a while now). I use this for my personal site.

Side note and caution to future generations: I recently discovered that the 50+ legal pads I filled with mathematics in grad school are completely illegible and worthless. Use pen, kids, not pencil!
posted by gleuschk at 8:08 AM on December 26, 2008

From the ease of setup, search, and offline criteria, I heartily second Evernote. You can even scan in hand-written notes and have the text searchable.
posted by gregchttm at 8:34 AM on December 26, 2008

Response by poster: I'd have thought that you already have a good solution, since you should be able to use Spotlight to search your notes. Can someone explain what using a wiki would add?

My main problem is that 1) spotlight (as far as I can tell) doesn't do a good job searching the text of .pdf files, so doesn't always pull up the paper I want; and 2) there's often a situation in which a later piece of work "modifies" a former one (e.g. shows that some guess I made in the earlier notes is incorrect) and in these settings I'd like to be reminded to look at the later thing whenever I look at the earlier thing.

But, given gleuschk's experience, it's possible that trying to be diligent about tagging these .pdf files as I save them, and possibly installing Google Desktop for search, might be just as good as wikifying.
posted by escabeche at 8:41 AM on December 26, 2008

Thanks, escabeche. I'm going to try Papers, which was recommended to me in a recent thread.
posted by lukemeister at 9:02 AM on December 26, 2008

Jacques Distler has hacked Instiki to support MathML.
posted by adamrice at 9:05 AM on December 26, 2008

Hey, how about using MediaWiki and the LatexDoc extension? An example of this can be seen here. Elsewhere on that wiki, the regular wiki maths notation is used also (although I am personally smitten with latex, hence preference for former).

With regards to your criteria though,

* I suppose it would fail on ease, unless you don't mind investing perhaps 2 hours in initial setup; little maintenance after that though.
* You can just use google for search, and this will search through the pdfs as they're in latex online too or the internal search engine.
* Finally, being in latex, it'll export well (as well as being online) and will be accessible in the future (no vendor worries).

Oh yes, and you'd have a history of changes, which could be handy too and since you're a mac, using safari, the pdfs would be embedded into browser.

Another link or two about this, in case you're interested in any case.
posted by jhayes at 12:21 PM on December 26, 2008

Oh yeah, I forgot about Instiki. It's pretty nice.
posted by gleuschk at 12:56 PM on December 26, 2008

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