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EMBL BioImage Data Analysis

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Timeline of @cmci_

cmci_ avatar

RT @biomicugm: Topics: Biostatistics, computational evolutionary biology, computational genomics and proteomics, graph models, image analys…
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @JustinMCrocker: We are looking for an interdisciplinary EIPOD postdoc to join our group @EMBL! Potential projects with @Eileen_Furlong,…
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @BioImagingUK: This maybe of interest to the @NEUBIAS_COST @openmicroscopy communities #imageAnalysis #imagingScientist https://t.co/I5
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @BioImagingUK: Software developer position on large image data analysis - working closely with the lab of @bayraktar_lab @sangerinstitut…
About 1 week, 2 days ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @AssafZaritsky: Modeling the interplay of lamellipodial motion and the intercellular actomyosin cable during epithelial wound healing h…
About 1 week, 2 days ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @jytinevez: @florianjug says be careful when using #CARE for intensity based quantification; CARE restoration is like a non linear trans…
About 1 week, 4 days ago by: Kota Miura (@cmci_)
blogtng:blogtop
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CMCI weblog

Finally managed to fix a blog bug

I always was disturbed by the appearance of single blog entry in this site that the body text was always shifted all the way down the page, that when one clicks an entry from a list of blog entries, one would not recognize that the text is actually there (I know by myself so it was no problem but for others…).

So after a year of using Dokuwiki, I finally decided to debug it. Since I am not a web programmer and not knowing how php is working, I used Firefox add-on called Firebug. Great convinient feature of this developer tool is that you could live-update CSS to see what will happen to the page. Especially, you could turn on and off specific attribute just by clicking.

This made me a way through complex Dokuwiki system to find out what was causing the body text shift-down problem. The part I edited was actually only a line in style.css line 238, attribute “clear both;”.

jsMath plugin installed

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.

Blocking spam

There has been Spam comments rushing in so I set the comments to be only available through CAPTCHA.

Dokuwiki Configuration: URL cleaning

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 ('/').

entry generator

Weblog Archive

blogtng/blogtop.txt · Last modified: 2016/05/24 05:46 (external edit)