Older blog entries for mbanck (starting at number 58)

I am currently sitting in the train to Goslar, where the German Conference on Cheminformatics will take place. As part of the Free Software Session, I will give a session on DebiChem. This is the first I attend this conference and I am looking forward to meet Noel O'Boyle and hopefully others from the community.

In light of this, I have packaged and uploaded RDKit and Cinfony over the last weeks and also updated the Debichem task pages, introducing a Cheminformatics Task at the same time. I feel we still need at least tasks for Chemical Education (to expose e.g. Kalzium more prominently), and possibly Protein Docking and Crystallography. So if you have experience/opinions in these fields (or want to propose other fields), drop me a mail or contact us at debichem-devel@lists.alioth.debian.org.

Woodchuck and FrOSCon

At the end of August, I attended FrOSCon in Bonn again, after skipping it last year. The evening before FrOSCon however, I visited Neal Walfield, his wife Isabel and their little son Noam in Düsseldorf. Besides having a great time and a lovely dinner, I was most impressed by their collection of Maemo devices (they had at least two N770s, an N900 and, to my jealousy, an N950) which Neal is doing research on these days. He works on woodchuck, which is a project investigating how to improve data availability on mobile devices and our conversation prompted him to implement ATP Woodchuck, which makes smarter decisions when to run APT upgrade on your Maemo device then the standard updater. As part of the research, they also run a user behaviour study which I joined, where one installs a client which records various data off your N900 and sends them anonymized (he seems to be doing a good job at that) to figure out how people use their mobile devices and hopefully enhance the experience. So if you have a N900, you should consider joining the study so they get better data.

The next day, I picked up Martin Michlmayr nearby and we headed for FrOSCon. I was quite impressed by the Makerbot at the Tarent booth, but I still don't know what they are really doing and why they had it on display... In the afternoon, I attended a couple of talks in the PostgreSQL developer room and a talk about a big OpenVPN deployment, before ending the day with the excellent as always social event barbeque. On Sunday, I went to quite a few talks, but I thought that two of them were particularly interesting:

Michael "Monty" Widenius of MySQL gave a talk titled "Why going open source will improve your product" about starting businesses on an open source project, or how business can/should open-source their product. Besides a detailed discussion about the various forms of Open Source licenses and the Open-Core model, he proposed the idea of "Business Source" (see slide 20 of his presentation), where a startup would distribute the source code under a non-commercial (but otherwise open-source) license with the explicit guarantee that the license would be changed to a true FLOSS license at some defined point in the future, giving the company a head start to develop and nurture their project. I asked whether this has been already implemented in practise and how the community could be sure that e.g. lawyers after a hostile takeover would not just remove that part of the copyright notice, as long as a true distribution under a FLOSS license has not happened yet. Monty wasn't aware of any real-word cases, and he did not seem to be concerned about this and said the original intent would be clear in a possible court case. This was the first time I heard about this approach, I wonder how other people think about it, whether it would work in practise and be a useful thing to have?

Second, I attended a talk by Gregor Geiermann, a Ph.D. student in linguistics on "Perceptions of rudeness in Free Software communities". He conducted an online survey about the perceived rudeness of several forum thread posts on Ubuntu Forums. Survey participants were first asked a couple of generic questions about their gender, nationality etc. and were then presented with a series of posts. For each post, they were asked to rate how rude they thought it was on a scale of 1 to 5 and they also had the possibility to highlight the parts of the post they considered rude as well as add comments. He presented a neat web application for analyzing the results, which makes it possible to select different groups (he did male vs. female and Americans vs. Germans in the talk) and have their overall rudeness ratings as well as the highlighted texts visualized as different shades of blue. Comments can be easily accessed. There were quite a few interesting differences e.g. in how Germans perceived rudeness compared to Americans (RTFM comments were considered less rude by Germans for example, IIRC). In response to my question, he said he intended to release the web application as open source and this might be an interesting tool for FLOSS projects to analyze how their public communication channels are perceived by various groups. Unfortunately, I cannot find any other resources about this on the web as of today, so I should try to contact him about it at some point.

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) »

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.

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