Using Wikis to organize
Why I like using a wiki:
They allow you to organize your research notes, class notes, etc. in a very intuitive fashion. You can use the search function to find things, can easily link to your own documents or documents on the web, and can easily collaborate (if your wiki is online).
Why I like pmwiki:It’s easy, portable and lightweight.
Once you set up a local wiki, if you ever want to move it somewhere else, all you have to do is move one folder (basically).
Help documents are very easy – just use the search in the upper right corner of your wiki – it’ll search pmwiki help pages in addition to your own website.
How to install and run pmwiki locally (on your computer)
(I downloaded zip file, could probably download another one if you want)
Point your webbrowser to: http://localhost/wiki/pmwiki.php,
where the “wiki” part is whatever you named your extracted folder.
Hooray! Your wiki is set up and ready to use.
The editing syntax is the same as what’s used on Wikipedia. For easy editing tips, just click “edit” for a page, and at the bottom it’ll give you basic editing commands. For more complete editing, go here.
Some useful customizations:
PasswordsIf you want a global password to access any part of your wiki, go to: wiki > pmwiki.php
To set a password for a specific page or group (or to edit a page or group), check this page out.
Pmwiki supports LaTeX markups, although it’s not perfect. To enable on your wiki, first check this out.
Here’s the basic steps:
Download this zip file.
Unzip LaTeXMathML.zip package into your PmWiki's root folder so that
Then go to docs and copy the sample-config.php folder. Copy it, then go to your local folder and paste the copy there. Rename it config.php. Open using a text editor and add this line to the end of it:
Now whenever you want to include LaTeX in a wiki page, just use $ $ notation (as in LaTeX). Some, but not all, of the LaTeX stuff works, so you’ll have to experiment around.
If you assign Paths properly, you should be able to move your wiki and files, and keep all the links working with very little effort.
To assign a path, go to
Scripts > intermap.txt
Open it, at the bottom there should be a Path variable that is undefined. Set it to what you want. For example, if I set my path to:
Then when I make a link like this: [[Path:/Papers/Baggerly2009.pdf]]
It will open http://www.biostat.jhsph.edu/~hiparker/Papers/Baggerly2009.pdf
If you change websites, and just move all of your folders, then all you have to do is change the Path variable rather than go through and edit each individual link your wiki.
You can make more Path variables (for example, Path2). Just keep adding new ones to the end of the intermap.txt file.
Windows EOL Problems:
If you have Windows and have trouble with the EOL characters for the above steps, email me and I can send you better-formatted files. Or, if you know some way to fix this, let me know!
Other Wiki Options
MoinMoin Desktop Edition