For some period of time, I had to switch to my Windows installation when writing articles with references, because I keep my references database there and there is an extremely convenient add-on for MS Office to insert citations and format bibliography on the fly.

However, it is quite inconvenient to make/run programs/scripts under Linux, and then switch to Windows to describe the obtained results in the article-like form. Thus, I briefly investigated available citation managers for Linux.
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To cut the long story short: for the final evaluation, I had this line of control panels:

• SysCP
• Domain Technologie Control, DTC
• Virtualmin (also Webmin, Usermin)
• ISPConfig
• RavenCore (no longer developed)
• GNUPanel

SysCP: looks good to me (though demo isn’t functional), has customer billing module. Unsure as to where it is used, but most probably sponsors are also the users of SysCP. Majority of support forums are in German.

DTC: has no demo, only some screenshots. Has a set of packages for Debian lenny (which is a huge plus for maintenance and future upgrades). DTC is being developed by GPLHost, and is also used by GPLHost – so this is a live (used) distribution. Seems quite feature-rich.

Virtualmin claims to be the “world’s most powerful and flexible web server control panel”. Virtualmin offers 4 means to control it: Web, mobile device, command line, and remote API. There are both screenshots and demo. Has both GPL and Professional versions. GPL version has a number of limitations, comparing to Pro version. From what I’ve read about Webmin (all three – Virtualmin, Webmin, Usermin – are just different “layers” of server control), it is a framework with a number of “interface scripts”, which allow to control various services. As such, it is easily extendible, but is not monolithic – in the sense of module inter-dependencies and action triggers.

RavenCore was a promising CP.

GNUPanel is a year-old control panel, but has a news item on the front page (dated August, 17) promising new, completely rewritten release somewhere in October. By the feature list, looks promising. However, I need the panel right now, and even in October, that will be quite a rough release, not really used/tested anywhere, so not a good option as well. But GNUPanel is a panel to check in half a year for progress.

As the final choice, I had ISPConfig (which seems to be the best by people’s comments), and which is also quite widely used, and is easy to install onto Debian (at least the Perfect setup: Debian Etch says so), and DTC. I discarded Virtualmin (for the poor functionality of the GPLed version), RavenCore (for the lack of current descriptions and non-functioning demo), GNUPanel (which just isn’t ready yet), and SysCP (because ISPConfig seems better ).

As DTC has Debian packages (and will be easier to maintain/upgrade), I decided to try it first. I already have it installed (that’s easy, esp. if you first read the DTC Debian Express Setup). Later I might post my impressions from using DTC.

Update: DTC is indeed easy and pleasant to use. I had problems allowing FTP and SSH access using MySQL authorization, but at least FTP was an easy one to fix (SSH access with MySQL authorization is still unconfigured, but that’s a low priority for me). There is a minor concern about the files and directory permissions setup, but thanks to chrooted environment that is only minor concern. Use of a single Apache installation for hosting admin and serving user sites might be a sub-optimal decision, but it works. Traffic and disk space accounting are plain superb! Server memory use for the dtc-toaster installation is troublesome, but for a powerful RAM-my server that is not a problem (I now have about 800-900MiB RAM occupied, but that includes the XCache’s cache, quite big MySQL cache, and loads of Apache and PHP modules).

But I’m still willing to try other control panels. As I expected, GNUPanel hasn’t released anything yet; Ravencore‘s online demo is still unfunctional; ISPConfig has recently released RC (and their demo is working as it should and as it used to); SysCP is also up and running fast. If my little hosting service starts pouring in some cash, then I’ll try SysCP on my second server – to compare it with DTC, and choose one of them for further support/extension/localization.

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.