Older blog entries for mbanck (starting at number 56)

Debian Med Bioinformatics Sprint

Last weekend, I was at the Debian Med Meeting in Travemünde near Lübeck, thanks to an invitation by Steffen Möller and Andreas Tille.

It was a great opportunity to finally meet Steffen and some of the other bioinformatics people in Debian like Manuel Prinz face-to-face for the first time. Also, lots of upstream and related bioinformatics packagers from e.g. Biolinux were present as well, many of them from the UK.

I discussed with and helped some people about Debian packaging. There is a big push to get Debian packages done and integrated in Debian and Ubuntu, but often enough people are not exactly sure what the requirements are and what needs to be done. Hopefully, the sprint was successful to clear things up and move forward.

I also managed to finalize the initial Jmol packaging and uploaded it to Debian towards the end of the sprint. I plan to update the other bioinformatics related packages in debichem like pymol and openbabel as soon as squeeze is released.

Overall, it was a great weekend, many thanks to NERC and Debian for making it possible, and to Steffen Möller for organizing it!

11 Dec 2010 (updated 11 Dec 2010 at 23:12 UTC) »
On Cancun's Success and Wikileaks

The success of the international climate conference in Cancun appears to be a great (and desperately needed) leap forward in the struggle to preserve our climate. At least news sources in Germany marvel at the very much unexpected and bigger-than-hoped outcome of the final declaration.

However, I keep wondering whether this could also be the first big success of Wikileak's power: what if Cablegate's timely leakage of the US and China's double-game at the Kopenhagen summit has scared their delegations so much they did not dare to repeat the backstabbing of the climate conference a second (or thrice?) time - in fear of their actions being defaced another time next year?

If this was the case, one could either call this Diplomacy by Fear or Diplomacy by Transparency - I choose to pick the latter. And if it indeed turns out Wikileaks had been the prime source behind a success for our planet, nominating the organization for the Nobel Peace prize does not look so absurd to me as it did last week.

8 Aug 2010 (updated 13 Aug 2010 at 15:46 UTC) »

So, DebConf is over and it was a blast. I wanted to blog about my talks for a couple of days, but the conference was so great that I did not get around to it until now.

The unique thing about this year's conference were the outstanding contributions by non-Debian FLOSS people from the east coast. I am really glad the organizers decided to reach out to the communi ty and take this opportunity when a lot of great minds were just a couple of hours away. Also, discussing and hanging out with the local team people was so much fun and interesting that it was wor th the visit alone.

The venue was just perfect, the dorms were on campus, the cafeteria had an all-you-can-eat buffet, everything was in short walking distance and the Columbia campus is beautiful. I would have liked to go to a couple more places in the evenings, but hanging out in the Carman basement lounge with awesome people was just as good. A big thanks to Richard Darst, Biella, Micah and the rest of the crew.

The Debian GNU/Hurd talk went quite well, I was pleasantly surprised so many people made it to the Davis auditorium. I wanted to do the presentation on Debian GNU/Hurd (and I had it working before the talk), but as my notebook has a different resolution than the projector, I decided to play it safe and just show a d-i run in qemu. Nevertheless, Jeremie's wo rk on debian-installer is impressive, I got it installed on my ThinkPad without a problem (using qemu) and it automatically installed and setup grub2. Unfortunately, grub2 seems to be having issues when booting my notebook natively, but I got it to work with grub-legacy, including X and evince.

There were quite a few comments and I had interesting conversations afterwards with a couple of people. It is a shame Emilio Pozuelo Monfort (pochu) could not make it to DebConf to give the talk himself, he did lots of great work on porting packages and fixing the Hurd and glibc for various testsuites over the last couple of months.

My other talk about GOsa and FAI was a bit rougher, I scrambled to get FAI integration in GOsa to work based on Mark Pavlichuk'sinstallation scripts which I fixed up over the last couple of weeks to the point where one can install a client using the FAI simple demo classes (which I ported to GOsa's FAI LDAP). There were some problems with the demonstration during the talk and I guess it was a tough audience for a web-based admin tool but I hopefully got my point across that we should salvage this work done for the city of Munich. Indeed, I had great discussions with Andreas Mundt from debian-edu afterwards who posted a summary and call for discussion to the debian-edu mailing list.

Science and Math Track at DebConf10

This year's DebConf10 (which is great, by the way) at Columbia University, New York will feature Tracks for the first time. We had a Community Outreach track on Debian Day (to be continued by more awesome talks over the rest of the week), a Java track on Monday and an Enterprise track yesterday.

Tomorrow, Thursday afternoon, the S cience and Math track (which I am organizing) will take place in the Interschool lab on level 7 of Schapiro Center.

The Track will start at 14:00 with a short welcome from me, followed by presentations of debian-science by Sylvestre Ledru and debian-math by David Bremner.

At 15:00, Michael Hanke and Yaroslav Halchenko will present their talk on "Debian as the ultimate platform for neuroimaging research".

This will be followed at 16:00 by three mini-talks on "New developments in Science Packaging". Adam C. Powell, IV will talk about MPI, Sylvestre Ledru will present linear algebra implementations in Debian and finally Michael Hanke and Yaroslav Halchenko will discuss the citation/reference infrastructure.

At the end of track, the annual debian-science round-table will happen at 17:00, where David Bremner (mathematics), Michael Hanke (neuro-debian), Sylvestre Ledru (debian- science/pkg-scicomp), Adam C. Powell, IV (debian- science/pkg-scicomp) and myself (debichem) will discuss matters about cross-field debian-science and math related topics.

If afterwards there are still outstanding matters to be discussed, we can schedule ad-hoc sessions for science or math matters on Friday or Saturday.

See you at the science track tomorrow!

DebConf's Law

If you hang out with local team people at some place, they must not have to buy beer themselves.

Bug-Squashing-Party in Munich

We are organizing another BSP in Munich on the weekend of 17th/18th July. Like the last BSP, it will take place in the LiMux office in the city center. See the coordination page for further information and directions and in order to sign up for it.

Food and drinks for the event are partly sponsored by the City of Munich and this amount (100 €) has been again matched by credativ GmbH.

Contributions by non-DDs are welcome as always; the BSP will be attended by several Debian Developers who will be able to upload fixes. Attending BSPs is a great way to get involved in the Debian community!

We cannot guarantee crash space to people from outside Munich at this point, so if you want to attend please contact the Munich list (area-muc@teams.debian.net) beforehand or arrange your own accomodation.

We probably start the BSP at some point after 6PM on Friday evening already, but the main action will be on Saturday and Sunday. As usual, people should bring their notebooks and possibly an ethernet cable. Wireless will be present as well, but a certain bandwidth cannot be guaranteed.

Bug-Squashing Introduction

I also plan to give an introduction to bug-squashing at this month's Garching Debian Stammtisch, which will take place next Wednesday, July 14th in the campus-cneipe (or its beergarden) as usual (the monthly Stammtisch is always on the second Wednesday of the month). If you study/work in Garching and would like to attend the BSP, come to the Stammtisch for a tutorial (and beer)!

Debian Packaging Tutorial

Some time ago, I gave a tutorial on Debian packaging in the TechTalk series of the Open-Source- School. The audience seemed to be pleased with the talk, and as more people requested to attend than there were seats in the room, we decided to reprise the event on September 7th. Attendence is free, but you have to register (see the event page). There are still some places left at this point.

30 Apr 2010 (updated 30 Apr 2010 at 19:44 UTC) »
Science Track at Debconf10

This year's Debconf will probably have for the first time tracks pertaining to certain subjects. One of the proposed tracks will be "Math and Science and Debian" and I was asked to organize it.

We have some talk proposals already, and we will have a panel discussion about Debian science packaging between the major contributors of the various packaging teams, but more talks are welome! Talks could be about science with/on Debian, or Debian development in scientific fields.

Additionally, I would like to encourage contributions on three types of topics:

  • Success stories about using Debian for scientific research
  • New developments in basic science packages and their packaging policies, like MPI/linear algebra libraries, or Fortran compilers
  • Developing/maintaining scientific software with or in Debian as upstream developers/scientists

Full length talks are not required, we could split up each topic among a number of people depending on interest and submissions.

Talks can be officially submitted until the end of tomorrow (Saturday May 1st, 23h59 UTC), but even afterwards, if you plan to go to Debconf and would like to give a talk about Math, Science and Debian, please contact me and we will see what can be done. Especially contributions to the three topics above can be made later as the events will be registered already.

27 Feb 2010 (updated 1 Mar 2010 at 21:41 UTC) »
Debconf11

This evening, the final decision on which city will host Debconf11 next year will be taken.

For the last half year, mostly Andreas Barth, Jan-Marek Glogowski and I have been working hard to make the Munich bid as good as possible. One thing we wanted to make clear from the beginning was that we would go for a conference in the city center - not some conference center in some nearby village or in an industrial area far away from where the city life happens.

It was not easy, since the german-wide decision, we had to reshuffle venue plans a couple of times.

In the end, thanks to Jan-Marek, we managed to get an excellent venue offer. Our bid consits mostly of:

  • Venue: Computer Science building (recently built) of Munich University for Applied Science, we can get as much as we need, for free. The only thing we would have to pay for is additional security personell during the night.
  • Network: Leibniz Rechenzentrum is the operator of the Munich Research Network (MWN), the venue is connected with at least 1 GBits fibre optics, and the MWN is connected to X-Win at the same speed. This will be free as well.
  • Food: We can either take up the offer from the Studentenwerk, the organisation operating the university restaurants. Of course, the quality is not like in a Michelin-star restaurant, but I have eaten there for several years during my studies and it is on par with previous Debconf offerings. Alternatively, we could look into food catering.
  • Accomodation: We tend to go for hostels, similar to Edinburgh, probably 4-6 bed dorms. Munich is pretty expensive for lodging, so this is something we decided early on to keep the costs reasonable. Again, I think this is in line with previous Debconfs. Of course, hotels at a broad price range are available.

The biggest strong points about Munich are, in my opintion:

  • Our local team has lots of experience with Debian and Debconfs, as well as organizing conferences
  • We have government support via the LiMux-project, and the city mayor of Munich, Christian Ude, has agreed to be the patron of the conference
  • Munich is very easy to get to, both for european (via train or car) or american/asian attendees (via plane). The airport is one of the biggest in europe and has direct connections to e.g. Atlanta, New York, Boston, San Fransisco, Los Angeles, Sao Paulo and Tokio.
  • Network connection via LRZ/MWN/X-WIN should be superb, especially to Debian machines hosted at euro

It the end, it seems Banja Luka seems to have the stronger bid, especially due to their 150000 EUR governemnt sponsorship. We will see who wins, I believe we did the best we could.

Application Indicators: A Case of Canonical Upstream Involvement and its Problems

I always thought Canonical could do a bit more to contribute to the GNOME project, so I was happy to see the work on application indicators proposed to GNOME. Application indicators are based on the (originally KDE-driven, I believe) proposed cross-desktop status notifier spec. The idea (as I understand it) is to have a consistent way of interacting with status notifiers and stop the confusing mix of panel applets and systray indicators. This is a very laudable goal as mentioned by Colin Walters:

"First, +5000 that this change is being driven by designers, and +1000 that new useful code is being written. There are definite problems being solved here."

The discussion that followed was very useful, including the comments by Canonical's usability expert Matthew Paul Thomas. Most of the discussion was about the question how this proposal and spec could be best integrated into GTK, the place where most people seemed to agree this belongs (rather than changing all apps to provide this, this should be a service provided by the platform)

However, on the same day, Canonical employee Ted Gould proposed libappindicator as an external dependency. The following thread showed a couple of problems, both technical and otherwise:

  • It is proposed as an external dependency, not as a part of GTK
  • It is unclear how it will integrate with the GNOME3 Shell
  • It requires Canonical's notorious copyright assignment
  • It is licensed under the LGPLv2.1 or 3 specifically, not any later one

What I personally disliked is the way the Cody Russel and Ted Gould are papering over the above issues in the thread that followed. For examples, about point one, Ted Gould writes in the proposal:

Q: Shouldn't this be in GTK+?
A: Apparently not.

while he himself said on the same day, on the same mailing list: "Yes, I think GTK/glib is a good place" and nobody was against it (and in fact most people seemed to favor including this in GTK).

To the question about why libappindicator is not licensed as usual under the LGPL, version 2.1 or later, Canonical employee Cody Russell even replied:

"Because seriously, everything should be this way. None of us should be saying "LGPL 2.1 or later". Ask a lawyer, even one from the FSF, how much sense it makes to license your software that way."

Not everybody has to love the FSF, but proposing code under mandated copyright assignments which a lot of people have opposed and at the same time insinuating that the FSF was not to be trusted on their next revision of the LGPL license seems rather bold to me.

Finally, on the topic of copyright assignments, Ted said:

"Like Clutter for example ;) Seriously though, GNOME already is dependent on projects that require contributor agreements."

It is true that there are (or at least were) GNOME applications which require copyright assignments for contributions (evolution used to be an example, but the requirement was lifted), however, none of the platform modules require this to my knowledge (clutter is an external dependency as well). It seems most people in the GNOME community have the opinion that application indicators should be in GTK at least eventually, so having libappindicator as an external dependency with copyright assignments might work for now but will not be future proof.

In summary, Most of the issues could be dealt with by reimplementing it for GTK when the time comes for this spec to be included, but this would mean (i) duplication of effort, (ii) possibly porting all applications twice and (iii) probably no upstream contribution by Canonical. Furthermore, I am amazed at how the Canonical people approach the community for something this delicate (their first major code drop, as far as I am aware).

To be fair, neither Ted nor Cody posted the above using their company email addresses, but nevertheless the work is sponsored by Canonical, so their posts to desktop-devel-list could be seen as writing with their Canonical hat on. Canonical does not have an outstanding track record on contributing code to GNOME, and at least to me it seems this case is not doing much to improve things, either.

Tutorials at the Garching Debian Stammtisch

Munich traditionally used to have a lot of Debian Developers, but over the last couple of years quite a few of us who used to be students graduated and moved elsewhere or became very busy with their day jobs. We still meet for having a beer and a chat, but not as much as some years ago. We used to meet about once a month, but in 2009 we only managed to meet four times (however, we organized a Bug Squashing Party in November and had a special meeting as Lenny Release Party in February)

As the meetings are really rather informal and not necessarily very Debian related, it is difficult to attract new people this way. So Johannes Wiedersich and I decided to try a more hands-on approach by having a second meeting in Garching, in the student-run bar on the campus of the Technische Universität München (TUM). The idea was to get more of the local science, mathematics and computer science students (as well as possibly interested faculty members) involved.

We tried a first time about a year ago, but after two or three meeting in late 2008 and early 2009, we lost momentum. However, we began organizing the meetings again with the start of the winter term, and had two rather successful meetings so far. For the first meeting, we basically handed out some information on how to get involved locally (the Debian-Munich list, its subscription address, the wiki etc.) and discussed Debian in general and Debconf11 in Munich in particular. About half a dozen people showed up, and two of these attended the Bug Squashing Party later that month, and another one (a faculty member) got very active in Debconf11 organization. Thus, I was quite happy with the outcame of that meeting.

Some days ago, we had another meeting, and this time I was doing a live-tutorial on Debian package building. As Johannes was ill, we did not manage to announce or publicize the meeting well in advance, so only three people showed up. Still, I think it went rather OK, and we will be doing another Debian package-building tutorial for the next meeting, and possibly other turorials/workshops afterwards (ideas so far include library maintenance, Debconf, how the Debian community is organized and how to get involved in it). As doing a live-tutorial on one notebook is a bit difficult if you both have to type on it and people should see what happens, we will either use some extra hardware next time, or move to some nearby seminar room with a projector, this will be announced in advance.

So if you are on Garching campus or nearby and interested in Debian development (and Debian package-building in particular), come to the next meeting on January 13th! We decided to meet on the second Wednesday of each month, at 18h. Subscribe to the Debian-Munich list to get the invitation or watch out for the flyers on the campus.

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