I’ve tried it already under Windows, but as my main OS is Debian, I can’t use it

You can sign up for updates on Linux version.

After reading the Google Chrome book, it is a long time waiting for it to be released for Linux….

Also, I’m looking forward for the plugins to enhance Chrome. Although it did import my settings/passwords(?!)/bookmarks from Firefox, but it has no Foxmarks, AdBlock and some other goodies I’m now used to on all the computers I regularly use.

There’s a Debian-Med project, aiming to

develop Debian into an operating system that is particularly well fit for the requirements for medical practice and research

Debian-Med has several web sites/pages: one at Debian.org (descriptive), and the actual project’s website at debian-med.alioth.debian.org. There’s also debian-med wiki (for developers).

As of nowadays, Debian-Med has released a number of Debian packages, which are grouped into respective Debian Med Tasks. The Biology-dev task, for example, contains MCL and libsbml packages (among many others).

Check this project out - you might find that the software you need is already available as Debian package.

This post was stimulated by Steffen’s comment.

There’s a troubleshooter for Ubuntu, which (expectedly) works quite the same for Debian (lenny in my case).

I’m installing libsbml to make the iBioSim tool work under Debian GNU/Linux. First thing I had to do was to make Sun’s java interpreter do all the java interpretation work instead of gcj: sudo update-java-alternatives -s java-6-sun (this assumes you do have java-6-sun installed).

Installing libsbml moved me one step further, now I’m getting another error from iBioSim:

Exception in thread "main" java.lang.NoClassDefFoundError: biomodelsim/BioSim
Caused by: java.lang.ClassNotFoundException: biomodelsim.BioSim
        at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
        at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)

This yet has to be fixed somehow.

If Zhou Xin’s blog becomes for any reason inaccessible (or moves to his own domain), below is the extract of the instructions from his post on how to install libsbml on Debian/Ubuntu Linux:
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Simplest way to develop your custom Drupal theme is to start with some skeleton/wireframe theme.

In this post, I’m briefly reviewing 4 themes (atck, blueprint, framework, and zen), made specifically to serve as theme developer’s starting point. All 4 are listed with their features (as per Drupal project page of each one), with my personal “impressions” (not based on actual use experience, yet). There’s also my choice and order of preference for the 4 candidates at the end.
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With this post, I’m finally announcing the opening of the (mostly) functional COTRASIF web-tool, created for the genome-wide identification of promoter regulatory sequences (transcription factor binding sits, TFBS). You can learn more from the About and Help pages. For an example of use, see the Supplement page (article is currently being prepared; as soon as it’s ready, I’ll make it available).

If you are interested - have a look at the News page, where there is information on joining COTRASIF Google group. For non-public enquiries, please use my contact page.

Note: the problem of identifying eukaryotic transcription factor binding sites stays acute for many years in a row - see e.g. the most recent Eukaryotic transcription factor binding sites - modelling and integrative search methods.

Some things to be aware of when enhancing Drupal site with FLV video playing/conversion features.

• Setup wizard for the free JW FLV Media Player (and the JW FLV Media Player itself)
• Flash Video in Drupal 5: A complete multimedia tutorial to the flashvideo module
• actual flashvideo module page on drupal.org

I’m providing regularly updated compiled linux and freebsd ffmpeg binaries, and also described how to use ffmpeg on shared hostings if not all the required libraries (like libmp3lame) are present. However, the solution recommended might not “fit all”, so here is another one - simpler and even more portable/universal than setting LD_LIBRARY_PATH.
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NicEdit - lightweight inline configurable rich-text editor for the web. Can fit where both FCKEditor and TinyMCE are too clunky and monstrous.

As an update to WordPress anti-spam plugins, I highly recommend Spam Karma 2. For a time, it seems to be the ultimate protection. I turned off all the other anti-spam plugins (including Aksimet), and everything’s just perfect! SK2 gathers up to a thousand spam comments/trackbacks during a single week on this blog, and I never had a complaint from blog visitors on their inability to add a comment (though some did have to fill in captcha to post a comment with links).

And SK2 still works under WP 2.5! (SK 2.3 was released to support WP 2.1)

Kudos to Dave!

It would be a pity if this excellent plugin is abandoned and stops functioning in one of the upcoming WP releases.

Update: SpamKarma is now GPL (at google code).

This post provides several links which would be useful for the beginning Drupal developers, or developers deciding which CMS to use as the base for their next project. Also, strengths of Drupal are highlighted.

Intensively working with Drupal during the past two weeks, I find it to be an excellent tool, and also much more than a YACMS.

Now I think that Drupal is also a framework - providing invisible to developer caching, session handling, access control, theming, localization, and more. The minimal effort required to extend already huge Drupal functionality is to write your own module - and, if done right, your module will immediately benefit from all the bonuses Drupal provides.

But Drupal also really shines as a CMS! You can start with a free design theme, and without any PHP knowledge have your custom portal built within a week - with your own hands, if you desire! (Note: “within a week” is true, but only if you already know what exactly you should be doing; learning time is short, but it’s not within that same week.)

What makes Drupal so powerful? I’d say that beautiful core and numerous modules.

What Drupal has to offer?
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Is that only me, or WordPress is really leaning towards the Drupal ideology?

Here’s what I mean:

• user levels were changed to user roles - just like in Drupal
• now, instead of categories and just recently introduced tags, the word ‘taxonomy’ is used - which is a Drupal slang
• ‘widgets’ work just like ‘blocks’ in Drupal - even style IDs are assigned the same way, e.g. id=”widget subscribe_to_comments_widget”
• (add here the similarity you found yourself)

I wonder, what will be next. PHPTemplate support, as default theming engine?
Or no-backwards-compatibility policy?
Or, best for WP users, advanced Drupal-like caching and throttling techniques?

drupaldojo.com - at the moment of writing, has 42 video-lessons (screencasts) of developing with Drupal.

Drupal technical introduction
It’s quite old, but as it describes core functionality, it should be still actual.

Please comment if you know of any other good high-quality technical Drupal introductions/descriptions.

Note: this post is based on the comment by Simon, who generously shared his experience.

Step-by-step:

• Download the compiled ffmpeg with libmp3lame support (direct download links: older version ffmpeg.with.lame and newer version ffmpeg.2007-10-28.with-libmp3lame-support).
• Rename the downloaded executable file to "ffmpeg" (no extension), upload it to the directory on your server (in this example /home/myusername/).
• Download libmp3lame.so.0.
• Upload libmp3lame.so.0 to the same directory where you placed ffmpeg in.
• Create a php file with the following code (remember to change the paths to your own, where you actually uploaded binaries in previous steps):
  PLAIN TEXT
  PHP:

  1. <?php
  2. exec("export LD_LIBRARY_PATH=/home/myusername/");
  3. echo passthru("/home/myusername/ffmpeg -formats");
  4. ?>

• If you access that PHP file with your browser, you should be able to see a list of formats which are supported by ffmpeg, and if you find "EA libmp3lame" somewhere in the output, then it means you now can Encode Audio in libmp3lame!
• If that doesn't work for you: LD_LIBRARY_PATH can be a protected variable in PHP (you can check for this by searching for the "safe_mode_protected_env_vars" value in phpinfo() output). The workaround here can be to write your commands to a file from php, then chmod that file with 0775 permissions (rwx-rx-rx), and run the file through exec(). In this way, PHP is not changing the LD_LIBRARY_PATH, but telling the server to run a file, which tells the server to change it. This method worked for the original author of these instructions.

For passing arguments to the PHP wrapper script - check out PHP's $argv variable (more on this here). If you decided to use shell-script as a wrapper for "export LD_LIBRARY_PATH", then using $1, $2 etc will allow you to pass parameters to the shell script, e.g. in the example below

you could pass "input file" as first argument, "parameters" as second and "output file" as third to make such a wrapper script work.

Get it here.

It adds Referrer of the person who's leaving comment on your WP blog. May help to take the right action for seemingly legit, but really spam comments (e.g. if someone was just searching for blogs with enabled commenting to leave a comment with name linked to their biz-website).

Problem report at menalto forum. Another one, also with no solution.

I can confirm - URL rewrite + DHTML Album Select produces two forward slashes in the Matrix theme, in my gallery 2.2.4 setup, after a single use of the Recalculate button in Disk statistics tab in Statistics plugin from Community repository.
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ExpressionEngine (EE) by EllisLab (see dislaimer). EE is available both as free and as paid-for: free has somewhat limited functionality, but enough to start the simple news site or blog. ExpressionEngine is suitable both for content-centric and news-centric (blog-like) projects, though in my opinion it's more geared towards news/blog-like sites.
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Today, using memtest86, system speed test, hddspeed and some other DOS utilities for diagnosing and testing PC hardware, I decided to put together my own simple bootable utility CD disk. But first, I did some searching to find if something similar exists.

It does exist - Ultimate boot CD. That CD has numerous freeware testing and diagnosing utilities which will help you - if you are up to some good old (read "small fast") DOS utilities. And not that old, actually - modern hardware is supported.

The only modification I'll do to the Ultimate boot CD will be adding freeware Biew bin/hex viewer/editor. Surely, more utils to come - with original size of just 115MB, there's plenty of room to add extensions. You can even extend the CD image with non-free software, like Partition Magic.

P.S. To diagnose and fix software problems - have a look at System Rescue CD.

If you want to fetch emails from some of your POP3-enabled mail accounts to Gmail, there's a help article detailing the process. However, when using Ukrainian Gmail UI, clicking the link which should bring up the dialog box to add one out of maximum five Fetcher accounts, I got instead an offer to add the email address which I can use in the From field of my outgoing emails - and absolutely not a word about fetching emails from other POP3 accounts.

When I switched to English (UK) UI, everything went just as described in the help article, and I added one address to fetch emails from.

After fetching some mails, I switched back to Ukrainian UI, and - quite expectedly - the Fetcher part disappeared from the Settings/Accounts. Now I'm waiting to see if the Fetcher is nonetheless functional, or if it is also disabled... It's functioning! So the only thing which was really changing in this case was the portion of the Settings/Accounts page not displayed while using Ukrainian UI.

The moral of the story is: when you think that some functionality is missing in the Google service you're using - just switch to English UI!

It's actually possible to install gpedit.msc snap-in for MMC in Windows XP Home Edition. I found the list of necessary files on pagesperso-orange.fr (in French), which also had the archive of all necessary (again, French) files and the installation batch-file (download gpedit pour xp home.zip; copied from here, which was found using "gpedit pour xp home.zip" keywords).

It's easy to figure out what to do even if you do not understand French, but do know what gpedit.msc is for. However, here are some short instructions in English for manual MMC snap-in installation (batch file from the archive does everything automatically, but you'll have to edit and verify the batch file first):

• put these files:
  

  appmgmts.dll
  appmgr.dll
  fde.dll
  fdeploy.dll
  gpedit.msc
  gpedit.dll
  gptext.dll

  into %SystemRoot%\system32 folder (most often it's just c:\windows\system32)

• put these files:
  

  system.adm
  inetres.adm
  conf.adm

  into %SystemRoot%\system32\GroupPolicy\Adm\ (create if this folder doesn't exist)

• finally, run these commands one by one in the CMD window:
  

  regsvr32 gpedit.dll
  regsvr32 fde.dll
  regsvr32 gptext.dll
  regsvr32 appmgr.dll
  regsvr32 fdeploy.dll

That should make gpedit.msc callable as Start -> Run -> gpedit.msc.

Other language versions of the necessary files can be retrieved from corresponding-language installations of WinXP Professional; English version can also be downloaded from Microsoft ( e.g. here , or search for "Group Policy ADM Files" at microsoft.com). Also, you can extract necessary files from available Windows distributions: just don't forget, that "filename.dl_" is a compressed version of "filename.dll", and can be uncompressed by using XP-bundled extract command.

Some additional information (geeks corner):

1. a comprehensive list of the "Group Policy/User Configuration/Administrative Templates" settings in Windows XP Home Edition
2. there's also an extremely comprehensive Excel sheet, which maps numerous *.adm-file options to their registry equivalents - Group Policy Settings Reference (PolicySettings.xls). This file is for Windows 2000, Windows XP, and Windows 2003

Disclaimer: I do not know if modifying (enhancing) your WinXP HE in such a way is a violation of any EULAs. It's your own responsibility to check this out and comply with any such regulations. Also, be advised that modifying any settings using gpedit.msc on WinXP HE may render some parts of the OS inoperable (IMO).