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.

Update 2: here’s a KDirStat-based alternative, WinDirStat.

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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