For the COTRASIF tool, I’ve been using the Ensembl Compara database (since release 47) to automatically import into COTRASIF gene orthology mappings.

However, with the E!50 release, the Compara database was dropped.

Looking for another option to get orthologs from Ensembl (using martservice, via biomart.org), I tried using the standard query - selecting “Homologs” group on the “Attributes” page for a single species database, and then selecting appropriate second species to get orthology mappings.

Imagine my surprise, when not only in the interface, but also in the generated XML file I found attribute names like “cow_ensembl_gene” :-O

I only need 11 species at the moment, and excluding the sufficiently unique name mappings like “zebrafish - danio rerio”, there is a number of questionable mappings: “yeast” for S. cerevisiae (could be S.pombe), “rat” for R. norvegicus (could be R.rattus), “anopheles” for A.gambiae (could be some other Anopheles). Other mappings might be also non-unique, especially for people working with different species of the same genus.

Am I missing some system in this naming “convention”, or am I the only one who finds it strange?

Is there a way not to use “common species names” when importing orthology data from Ensembl with the help of martservice?

Found via Jason Calacanis weblog.

Please skip this post if you’re feeling workaholic: there is absolutely nothing useful inside.

See full post for videos.
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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
• GNUPanel

SysCP: looks good to me (they have a working demo), 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 is 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, if it had a working demo, could be an option. It seems to be quite actively developed, but all the screenshots are outdated, and demo isn’t working. However, based on what I’ve read, at least some people seem to be satisfied with this 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.

There’s a how-to on the topic at howtoforge.com.

Note, that for the suggested solution to work, NAT/firewall should be “transparent” for outgoing ssh connections.

2008 South Ossetia war

It has been quite a time since my last serious and long post. On the one hand, summer is vacations time - so I’ve been to one in Turkey; on the other hand - the long-awaited ICSB-2008 conference finally took place in Gothenburg, Sweden, on August 23-27 (or 22-28, counting in tutorials and workshops).

Synopsis: in this post I present a personal-perspective report on the 9th ICSB (with a condensed ICSB-2008 photo-report in my gallery).

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One of the benefits, offered exclusively by the Windows Vista Ultimate (not even by the Windows Vista Business), is

running UNIX applications (via SUA, Subsystem for UNIX Applications) , which provides higher flexibility for Windows workstations.

Where is the world going?

And how soon will all the Windows users (not only Ultimate Users) benefit from the higher flexibility by running UNIX applications?

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.

These are the addresses for those who would like to travel lightly, meet new people, get new friends, hang out with interesting people, or just find a shelter for a night in the foreign country.

I’m now registered in both systems (and getting “verified” in CS), and so far I stayed with three people (at two places) found via HC and CS. Both experiences were highly positive. Actually, my world outlook changed quite a bit after my first stay: I heard from someone that

it’s better to trust wrong person once, than always distrust all the people

But building trust, despite being central to HC ans CS, is only one - basic - component. Cultural exchange and knowledge sharing are also important, though so far I was unable to comprehend these components sufficiently to write on them.

At the CouchSurfing.com website, it appears to be popular to put some test/quiz results into profiles. These are the tests:
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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.