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).

Update: there’s now a much more recent post on how to install libmp3lame-enabled ffmpeg on shared linux hosting.

As Gabe pointed out in my post with compiled ffmpeg Linux binaries, there is a relatively simple method of adding libmp3lame.so.0 file to your shared hosting so that ffmpeg executable will see the library:

You can upload libmp4lame.so as well to the shared hosting site and when you call ffmpeg, call something to set an environment variable right before the call to ffmpeg i.e. in php I’d do exec(”export LD_LIBRARY_PATH=/path/to/lib/with/lame; /path/to/ffmpeg [ffmpegargs]”); That way you can use the uploaded lame. I hope that helps someone as I have been unable to find any info on how to use an uploaded lame. I’ve tried it and it works on godaddy.

Hope this helps.

Update: here’s libmp3lame.so.0.0.0 (from slackware 2.4.x, lame-3.97). I have no idea if it’ll work in your (shared hosting) environment; it is provided AS IS, use at your own risk etc. I can only state that the archived binary file at the moment of upload was indeed libmp3lame.so.0.0.0 from my elderly Slackware with 2.4.x kernel.

Cytoscape 2.5.1 supports proxies, including HTTP proxies, but there is no support for HTTP proxies requiring authentication/authorization. It’s easy to use Cytoscape in the authentication-requiring proxy scenario; below is one possible method.

Note, that exactly the same method can be used to allow any software, which supports proxies but not proxies with authentication, to be able to access the internet.
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When ‘make’ing krename (after ./configure, of course), it failed with an error message like:

libtool: link: `/usr/libGL.la’ is not a valid libtool archive

After reading this topic (in Russian), I found that libGL.la is a configuration file for libGL.so.
This configuration file is created when installing ATI or nVidia video drivers - they replace the bundled libGL.so and create libGL.la.

The solution to the “absent libGL.la” file is, thus, either to install ATI/nVidia drivers (if you have ATI/nVidia video card), or to manually create “fake” libGL.la.
Here is the sample of “fake” libGL.la (to copy-paste, click the “Plain text” header) :
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Today I was looking for some simple but convenient source-code editor. I came across this post, and decided to try Geany. I’m using Slackware 11 at the moment, and as there were no packages available, I downloaded Geany source to compile and install.

However, the ‘configure’ script failed. When trying to compile ‘conftest.c’ with gcc, the following error was produced:

libc.so: file format not recognized; treating as linker script

(Note 1: in the error above, I removed all the paths which were prepended to the actual error message.)
(Note 2: I suspect that this error is the result of incomplete/failed/erroneous update of glibc slackware package I attempted a while ago. Will have to fix that more properly than described below.)

Here’s the solution which helped me to install Geany successfully:
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Update: if you were looking for a downloadable libmp3lame.so.0, then go here or here.

Today I compiled ffmpeg with –enable-libmp3lame. Of course, first I downloaded, compiled and installed lame (libmp3lame) itself. However, after doing make install for ffmpeg, and then running ffmpeg produced an error:

ffmpeg: error while loading shared libraries: libmp3lame.so.0: cannot open shared object file: No such file or directory

I looked for libmp3lame.so and found one in /usr/local/lib (evidently, ffmpeg couldn’t see it there; ffmpeg was searching for libmp3lame.so.0 in /usr/lib/, not in /usr/local/lib/). It was clear that /usr/local/lib/libmp3lame.so is a symlink to /usr/local/lib/libmp3lame.so.0.0.0. So all I had to do was making one more symlink in /usr/lib/, pointing at /usr/local/lib/libmp3lame.so.0.0.0:

ln -s /usr/local/lib/libmp3lame.so.0.0.0 /usr/lib/libmp3lame.so.0

After this, ffmpeg ran without any problems.

Updated on Apr 8, 2008.

Stimulated by the post of Eric Daniel, I compiled the most recent ffmpeg SVN source into Linux binary, which runs fine on my shared hosting (note: I’m using older ffmpeg binaries, which are at the end of the post).

mini-FAQ:
Q: Why the title has “for Gallery2″?
A: Just because I avoided the inclusion of libraries, which were not found on my shared hosting server. I hope this will work for other shared hosting environments.

Configuration, version and date can be found in the output of ffmpeg.

Versions built on April, 8, 2008:
ffmpeg (no lame) (checked: can be executed on godaddy shared hosting)

FFmpeg version SVN-r12769, Copyright (c) 2000-2008 Fabrice Bellard, et al.
configuration: –enable-gpl –enable-postproc –enable-swscale –enable-pthreads –disable-debug –enable-gray –disable-ffserver –disable-ffplay –enable-avfilter –disable-network –disable-ipv6
libavutil version: 49.6.0
libavcodec version: 51.54.0
libavformat version: 52.13.0
libavdevice version: 52.0.0
libavfilter version: 0.0.0
built on Apr 8 2008 15:13:14, gcc: 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)
usage: ffmpeg [[infile options] -i infile]… {[outfile options] outfile}…

ffmpeg (with lame). For this one, grab libmp3lame.so.

FFmpeg version SVN-r12769, Copyright (c) 2000-2008 Fabrice Bellard, et al.
configuration: –enable-gpl –enable-postproc –enable-swscale –enable-pthreads –disable-debug –enable-gray –disable-ffserver –disable-ffplay –enable-avfilter –disable-network –disable-ipv6 –enable-libmp3lame
libavutil version: 49.6.0
libavcodec version: 51.54.0
libavformat version: 52.13.0
libavdevice version: 52.0.0
libavfilter version: 0.0.0
built on Apr 8 2008 15:44:31, gcc: 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)

Based on single request: ffmpeg (with lame and libfaac and libfaad). For this one, grab libfaac.so and libfaad.so.

FFmpeg version SVN-r12769, Copyright (c) 2000-2008 Fabrice Bellard, et al.
configuration: –enable-gpl –enable-postproc –enable-swscale –enable-pthreads –disable-debug –enable-gray –disable-ffserver –disable-ffplay –enable-avfilter –disable-network –disable-ipv6 –enable-libmp3lame –enable-libfaac –enable-libfaad
libavutil version: 49.6.0
libavcodec version: 51.54.0
libavformat version: 52.13.0
libavdevice version: 52.0.0
libavfilter version: 0.0.0
built on Apr 8 2008 23:53:57, gcc: 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)

As an experiment, here’s ffmpeg freebsd binary without lame support. Did ran on some FreeBSD 6.3 hosting.

FFmpeg version SVN-r12769, Copyright (c) 2000-2008 Fabrice Bellard, et al.
configuration: –enable-gpl –enable-postproc –enable-swscale –enable-pthreads –disable-debug –enable-gray –disable-ffserver –disable-ffplay –enable-avfilter –disable-network –disable-ipv6 –target-os=freebsd
libavutil version: 49.6.0
libavcodec version: 51.54.0
libavformat version: 52.13.0
libavdevice version: 52.0.0
libavfilter version: 0.0.0
built on Apr 8 2008 16:15:38, gcc: 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)

Versions built on Ocotber, 28, 2007:
download ffmpeg without libmp3lame support

FFmpeg version SVN-r10867, Copyright (c) 2000-2007 Fabrice Bellard, et al.
configuration: –enable-gpl –enable-pp –enable-swscaler –enable-pthreads

–enable-libogg –enable-libvorbis –disable-debug
libavutil version: 49.5.0
libavcodec version: 51.47.1
libavformat version: 51.17.0
built on Oct 28 2007 22:46:10, gcc: 3.4.6

download ffmpeg with libmp3lame support

FFmpeg version SVN-r10867, Copyright (c) 2000-2007 Fabrice Bellard, et al.
configuration: –enable-gpl –enable-pp –enable-swscaler –enable-libmp3lame

–enable-pthreads –enable-libogg –enable-libvorbis –disable-debug
libavutil version: 49.5.0
libavcodec version: 51.47.1
libavformat version: 51.17.0
built on Oct 28 2007 23:04:59, gcc: 3.4.6

Shared hosting testing reports are welcome.

Below you can find even older versions of ffmpeg, which were tested and found functional on GoDaddy shared hosting.
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Full Featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows.

Small and convenient. Can do sequence alignments (I recommend to limit the length to 2kb for alignments).

Latest version I found: updated July, 2001, GeneDoc version # 2.6.02.

Drawback: windows only (but has GNU-licence sources).

Jpegtran is a library for lossless rotation and cropping of JPEG photo files. Ffmpeg is a library for some basic video processing and playback. Gallery2 is a powerful and popular photo-gallery web-software.

Gallery2 uses by default either PHP’s GD2 or ImageMagick toolkits to rotate/crop images. However, you can install jpegtran plugin, to rotate/crop JPEGs with no losses in quality.

On GoDaddy shared hosting the path to jpegtran is /usr/bin/jpegtran. However, at least in my case, that binary failed the ‘crop’ test (but succeeded in ‘rotate’ test). So I downloaded another binary of jpegtran (from this page), put it into one of my folders, and told Gallery2 to use that binary instead of /usr/bin/jpegtran. This worked perfectly.

The same approach can be used to enable thumbnails for videos via the ffmpeg plugin and binary (unfortunately, have no idea where did I take ffmpeg from - it was quite a time ago). Just download the binary, put it into one of your folders, tell Gallery2 the absolute path to the binary, and you are done!

Finally, here are the links to the two binaries mentioned above:
jpegtran
ffmpeg

ffmpeg update: see here.

I’m planning to reconstruct (based on literature and some original research) a specific cellular regulatory network. For this I decided to use some specialized biological modelling software. The requirements I had were pretty simple:

• must have SBML support. SBML appears de-facto standard for biological model notation;
• must be fairly frequently updated;
• should be feature-packed and easy to use. However, this requirement can only be checked after some use, and I was pre-selecting, not reviewing.

Software put into the title of the post was found to be the most mature and interesting from the usage perspective. However, there are more than those mentioned software tools reviewed. Reviews are based primarily on the information from official websites and documentation; some tools (like VirtualCell) are reviewed somewhat more thoroughly.
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I think Sequoia View is a must-have utility program.
“Why?” - you may ask.

Because it lets you actually see you hard disk hogs. With this program you will know exactly which files/folders occupy too much hard disk space to keep them any longer.

The program is free, latest version is 1.3 and it was released in November 2002. However, WinXP is supported (don’t know about Vista).

See this page for more information and the download link.

Alternatively, contact me and I’ll try to mail you the setup program (which is circa 500KB).

Update: SequoiaView appears to ignore files larger than or equal to 4 GiB. Please comment to prove or disprove.

Recently I learned about Zope, which is an “open source web application server”, primarily written in Python.

Then Django and Turbogears were seen as web-development frameworks akin to Zope. Search revealed an interesting anti-Zope rant at Zope vs Django. Reading until the end, and then following the comments, I came across the comment by Holger Froebe, which is a huge one (probably the longest comment I had ever seen), and represents a detailed explanation with examples of the reasons to use Zope 3. I found that comment to be a really good-written one, so if you are deciding on whether you should use Zope 3 or not, then read the comment here (scroll down or just search for “Holger Froebe”).

For convenience and in order to preserve this worhty piece of work from vanishing, below is the 99%-exact copy-paste of that comment.
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After IE7 came out, it got much harder for HTML/CSS coders to maintain compatibility with both IE6 and IE7.
IE7 is pushing IE6 out, as it is a high-priority update; however, massive part of users will remain on IE6 for various reasons, not excluding the licensing issues (non-licensed/fake-licensed Windows XP will not let install IE7).

The problem is: after installing IE7, you no longer have IE6 (which is replaced by IE7).

However, there is a good and simple solution, enabling one to run IE3 through IE7 on one computer.
To do so, just install the latest version of IE you want (I assume it’s IE7), and then point your browser to evolt’s archive of browsers (what an excellent collection!). You will have to “install” (just copy, really) each older IE you want into a separate directory, and create a short-cut for each. (You may want to use all-in-one installer, found here - also a great package, though I didn’t use it.)

After I installed IE6, I also copied some additional files to its folder (like wininet.dll, version 6.00.2900.2180 or like that), to avoid problems with cookies disabled in IE6.

However, there is a huge problem with multiple IEs: Print Preview and Print do not work at all!
After some searching, I found two bug reports:

• clicking on any bookmark will not load the bookmark, but will open the Print dialogue
• trying to use the bookmark-derived Print dialogue appears not to work: produces blank page

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I’ve been using PhotoFiltre for quite a while until now, and can recommend this software.
In my case, primary usage purpose is light-weight editing - when Photoshop/GIMP would be an overkill, and Paint is just not enough.
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In my previous post on project management tools I stated that will try dotProject out. So I did, and here are my first impressions (mostly - what I dislike; the likes will come after some period of usage).
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In one of my recent posts about project management software I stated the desire to extensively test dotProject 2.0.4. However, GoDaddy.com shared hosting appears incompatible with dotProject: the right to CREATE TEMPORARY TABLES in MySQL is not granted, but is needed by dotProject.

Here’s sample error:

query failed(CREATE TEMPORARY TABLE tasks_sum SELECT task_project, COUNT(distinct task_id) AS total_tasks,
SUM(task_duration * task_percent_complete * IF(task_duration_type = 24, 8.0, task_duration_type))/
SUM(task_duration * IF(task_duration_type = 24, 8.0, task_duration_type)) AS project_percent_complete FROM `tasks` GROUP BY task_project)

I tried looking for solutions, and here’s what I found…
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I decided to streamline my project management procedures with some kind of software, as the number of concurrent projects is increasing, and more and more time is lost both for switching tasks and trying to grasp a-new the global view of the project each time I turn to it.
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