Installed jsMath plugin, for using tex code directly in this wiki. Some problems seems to appear with previous text with .htaccess codes, but will fix later.

further notes: 2010 Apr. 21
I initially used jsMath to show math equations but then realized that mathJax is more up-to-date module for doing this (mathJax actually is de facto jsMath2.0). I then switched to mathJax.

MathJax works well with Chrome when you view this page. But then soon I found out that this is possible with only Chrome, not with Firefox nor IE. Since most of people visiting this site use Firefox, I started to try configuring but did not work with many different trials… then finally I found a solution for Firefox; upgrade it. The problem I had in viewing math equation was occurring with version 3.0x (on win32), and this does not happen and works well when version 3.6.3 is used. It was as simple as that. without thoughts, I was thinking that “My Firefox should be pretty new”.

The problem I encountered seems to be due to difference in the web-font loading settings. With IE, one better try to use at least IE9. I have not tired this yet, and probably will not because I have not seen any visitor using IE these days.

By the way, if you want to test if your browser is enabled with viewing math equation in cmci.embl.de, click the link below to test if it is possible.

http://cmci.embl.de/mathjax/test/

note:20110526

a disadvantage after installing jsMath plugin is that the page loading became significantly slower than before.

There is always some confusion when deriving Diffusion coefficient after Soumpasis fitting in FRAP, whether to use radius or diameter for the parameter “w”. As manual has been saying, this “w” is indeed radius, not diameter. I made a bit of stress on this part.

http://cmci.embl.de/documents/frapmanu

In local.php (not accessible so configured through configuration manager)

   $conf['userewrite'] = '1';
   $conf['useslash'] = 1;

Copied .htaccess.dist to .htaccess, then in .htaccess, *une-**commented out lines shown in Red

14 ## Uncomment these rules if you want to have nice URLs using
15 ## $conf['userewrite'] = 1 - not needed for rewrite mode 2
16 RewriteEngine on
17 #
18 ## Not all installations will require the following line. If you do,
19 ## change “/dokuwiki” to the path to your dokuwiki directory relative
20 ## to your document root.
21 RewriteBase /
22 #
23 ## If you enable DokuWikis XML-RPC interface, you should consider to
24 ## restrict access to it over HTTPS only! Uncomment the following two
25 ## rules if your server setup allows HTTPS.
26 #RewriteCond %{HTTPS} !=on
27 #RewriteRule ^lib/exe/xmlrpc.php$ https://%{SERVER_NAME}%{REQUEST_URI} [L,R=301]
28 #
29 RewriteRule ^_media/(.*) lib/exe/fetch.php?media=$1 [QSA,L]
30 RewriteRule ^_detail/(.*) lib/exe/detail.php?media=$1 [QSA,L]
31 RewriteRule ^_export/([^/]+)/(.*) doku.php?do=export_$1&id=$2 [QSA,L]
32 RewriteRule ^$ doku.php [L]
33 RewriteCond %{REQUEST_FILENAME} !-f
34 RewriteCond %{REQUEST_FILENAME} !-d
35 RewriteRule (.*) doku.php?id=$1 [QSA,L]
36 RewriteRule ^index.php$ doku.php

and also changed line 21, specified the base directory ('/').

Old CMCI is now moved to new wiki format (dokuwiki), to make the editing more efficient and also to involve more people editing and exchange information.

Previous site could be found below:

http://cmci.embl.de/oldindex.html

Most of contents were migrated from old to new as it was.

— changed main.php to add logo at the top right corner (Manuela's suggestion, thanks)