Thursday, 28 November 2013

Bits from Debian Med team (by Andreas Tille)

Some of these bits are a bit outdated but there is no point in hiding this information just because it is old.


Andreas Tille had a talk at FOSDEM which is also Video recorded. A quite similar but updated talk was held at DebConf 13 (see below).

Jabber interview by reporter from India

There was an interesting interview between Rajeev Nair and Andreas Tille at So, 17.02.2013 Rajeev Nair is Business head of an health care journal in India held via jabber. Since this might serve as some nice FAQ about Debian Med here is a complete log of this interview (permission to publish it was granted).

Article about Debian Med

As a consequence of the interview above the Debian Med team has assembled an article which was originally intended to be published in the Health Cafe journal but somehow this never happened. So we ended up with a nice article targeting at interested readers about Free Software in medicine with not necessarily informatics background. Since the article is considered to be of good quality and has consumed some time of several team members we are seeking for ideas for relevant places where to publish it. It is available as PDF as well as in SVN.

Yearly sprint of Debian Med team

This year we had our third sprint of the Debian Med team and all participants consider it a great success again. The sprint was in end of February and the individual reports are linked from the according wiki page. Since Andreas Tille was able to prove the nice effect of having face to face meetings in Debian teams in the team metrics graphs presented in his talks at DebConf (see below) we will keep on with this good tradition. The next sprint is scheduled for Friday 31st January until Sunday 2nd February in Stonehaven near Aberdeen. If you are interested to meet the people behind Debian Med and want to join us in developing packages which are helpful in health care and bioinformatics you are invited to join us.

DebConf 13 in Vaumarcus

Andreas Tille had two talks with specific influence to Debian Med development(Debian Med as a success story for other Blends, How to attract new developers for your team (MoM, SoB). For those who want to read a full (and lengthy) report about DebConf 13 by Andreas Tille this is online in this blog article.

Codefest of the Open Bioinformatics Foundation

Ivo Maintz and Steffen Möller organised the Codefest of the Open Bioinformatics Foundation in Berlin. About 40 contributors from all over the world attended, connecting the Debian community strongly with upstream. The event triggered a joint paper of participants to Sprints, Codefests and Hackathons alike, presented at the Nettab conference on Semantic, Social, and Mobile Applications for Bioinformatics and Biomedical Laboratories in Venice.

Reupload unattended packages

Andreas Tille has mentored the GSoC student Emmanouil Kiagias and as a byproduct some Blends metadata were now kept in UDD. This has inspired some new tools and one of this was an UDD query to return all packages in the interest of the Blend ordered by date when they were uploaded. It has shown that there were packages hanging around in the package pool since five years. So some effort was done to check those packages which were not necessarily "buggy" according to BTS entries and so we were able to fix the following issues in about 20-30 packages:

  • Remove DM-Upload-Allowed fields
  • hardening
  • canonical Vcs fields
  • checking homepages / watch files
  • checking policy 3.9.4 (cme fix dpkg-control)
  • profit from xz compression in binary packages which makes perfectly sense in some of our packages
  • DEP5
  • DEP3
  • use dh consequently to simplify things for team members / NMUers
  • finally upload several changes in VCS but remained UNRELEASED
  • found several other hidden issues like
Since it was impressive how many things that deserve fixing are hidden in such long unattended packages it is recommended also to other teams to spend some time into these. The UDD query can be easily tweaked for a team maintainer address.

Debian Med Bug Squashing Advent Calendar 2013

The Debian Med team will again do the Bug Squashing Advent Calendar. Feel free to join us in our bug squashing effort where we close bugs while other people are opening doors. :-)

Kind regards and see you at Debian Med sprint

Monday, 16 September 2013

DebConf 13 report (by Andreas Tille)

General impression

 Scenic Hacklab I'm beginning my DebConf report in an unofficial "Scenic Hacklab" right at the edge of the lake in Yverdon. This is the right place to memorise the last days. When I started from this place cycling to Le Camp 12 days ago I was full of great expectations and what should I say - the reality has even beaten these.

Once it comes about comparing DebConfs even if it is an unfair comparison due all the differences my secret long term favourite was Helsinki very closely followed by Argentina and also very closely followed by all the other great DebConfs I joined (and I joined all in Europe). Would Le Camp be able to beat it? The short answer is: Yes, it is now my favourite DebConf while I think I do not suffer from the last-Debconf-was-the-best-DebConf-syndrome (and I realised there are others thinking the same).

As you might probably know I'm a bit addicted to swimming. While Helsinki had admittedly the better conditions I was at least able to fix the distance issue using my bicycle. (Hey, those Le Camp photographers did a great job in hiding the fact that you can not actually touch the lake right from the meadow of Le Camp.) Being able to have my bicycle at DebConf scored some extra points. However, the really great view of the lake, the inspiring "Scenic Hacklab" which was my favourite place has bumped DebConf13 at first place in my personal ranking.

So it comes quite natural to say: "Kudos to the great organisation team!" They did a Swiss-like precise work and perfectly succeeded in hiding any problems (I assume there were some as always) from the attendees so everything went smooth, nice and shiny for the attendees. The local team was even precise in setting up great weather conditions for DebConf.

sunrise over
 the lake While saying thanks to the local team I would like to also explicitly thank Luca Capello who has quite some share that this DebConf was possible at all (while I have to decrease my DebConf score one point because he was not really there - Luca to bad that you were not able to come full time!) Also thanks to Gunnar and Gannef who helped remotely (another score down because I were missing them this year as well).

Even if it was my favourite DebConf I was not able to work down my todo list fully (which was not only uploading one package per day which I at least statistically fullfilled). But that's probably a general feature of todo lists anyway. One item was definitely done: Doing my daily swimming BoF. I actually was able to do the other parts of the triathlon which was skipped by Christian and have done in summary about 150km cycling with 3500m elevation and estimated 7-8km swimming (0m elevation ;-)). Considering the great view at sunrise over the lake I was not hating my "Senile bed escape" disease too much (I was every day waking up at sunset) - it was simply a great experience. I will never forget seeing water drips glimmering like gold inside the morning sun while seeing the Alps panorama in the distant. I hope I was able to help all interested swimmers with the DebConf Beach Map which was just a by-product of my activities in DebCamp.

Speaking about OSM: I was astonished that the area was way less covered than I expected. Thanks to several DebConf attendees the situation became better and the map does not only show random trees in the wild but also the tracks leading to these. (Remark: It was no DebConf attendee who is responsible for plastering the map with single trees.) While I had my mapping focus basically close to the edge of the lake I was also able to even map my very own street. :-)

I clearly remember one specific mapping tour when I was invited by the DPL: He convinced me to join him on a bicycle tour and since I was afraid to get fired I joined him instead to keep on hacking. Also Sorina was brave enough to join us on the tour and she did quite well. (Sorina, do you remember the agreement about your work on the installer? ;-)) Lucas described the tour as: going uphill on only asphalted roads. Sorina and me were witnessing the mighty DPL powers when we left the wood around Le Camp to reach the described road: The asphalt was just put onto the road - no doubt that it was done on the immediate demand of mighty DPL. :-)

DebCamp time was flying like nose dive and a lot of known (and unknown) faces arrived at Le Camp. What I really liked a lot this year was that several really young children has pulled down the average age of DebConf attendees. I clearly remember all the discussion one year ago what to do about children. As always the issue was solved in a typical Debian way: Just do it and bring your children - they had obviously a great time as well. I think the youngest child was 2 months and the oldest "child" above 20. ;-) Actually Baptiste Perrier did great in making the C&W party a success and had obviously a nice time. (I wished my son would have been able to come as well but he needs to write his bachelor’s thesis in physics. :-()

It was nice to see the kids using all playing facilities and communicating with geeks. Also I would like to point out that even the very young attendees had their share at the success of DebConf: Just think of the three "bell ringing assistants" who helped me ringing the bells for lunch and dinner. I've got this cool job from Didier in the beginning of DebCamp. I must say having some real bells ringing is by far nicer than just the "lunch / dinner starts in 10 minutes" from IRC bot. The only thing I did not understand was that people did not considered ringing the bells at 8:00 for breakfast as a good idea.

Regarding the food in general I would also like to send kudos to the kitchen: It was tasty, freshly prepared, regional food with a good change rate. I really liked this. Extra points for having the chance to sit outside when eating.


But lets have a look into the conference programme. I'd really recommend watching the videos of the talks Bits from the DPL (video) and Debian Cosmology (video). I considered both talks as entertaining and interesting. I also really hope that the effort Enrico Zini started in Debian Contributors (video) will be successful.

I had some talks and BoFs myself starting with Why running a Blend (video) and I admit that (as usual) the number of attendees was quite low even if I think there is some proof (see below) that it is interesting for way more people who should consider working more "blendish" in their team. Do you know how to recruit one developer per year and relax the man power problem in your team? Feel free to watch the video. We have confirmation that ten DDs of our team have considered to join Debian only because Debian Med exists. Admittedly biology and medicine are really leaf topics inside the Debian universe. So if even this topic that has a very tiny share of the Debian users is able to attract this level of attention - how many more people could we win for multimedia, games, GIS and others?

So if you feel you are quite overworked with your packaging and you have no time this is most probably wrong. The amount of time is basically a matter of priorities you set for your tasks. Try to put some higher priority onto using the just existing Blends tools I explained in my talk to attract more users and developers to your team and by doing so spread the workload over more people. It works, the prove was given in my main talk. So before you start working on a specific package you should wonder who else could have an even stronger interest to get this work done and provide him with some additional motivation and help to get the common goal done.

The interesting thing is that my BoF about How to attract new developers for your team (video) - which was a simple report about some by-product of the Blends work - made it into the main talk room and got way more attention. For me this is the proof that the Blends concept itself is probably badly perceived as something like "a few outsiders are doing damn specific stuff which is not really interesting for anybody else" instead of what is really is: Smoothing the way from specific upstream applications to the end user via Debian.

Once you see the video of this BoF you can observe how my friend Asheesh Laroia became more and more excited about the Blends concept and admitted what I said above: We should have more Blends for different fields. Funnily enough Asheesh asked me in his excitement to talk more about Blends. This would have been a really good suggestion ten years ago. At DebConf 3 in Oslo I had my very first talk about Blends (at this time under the name "Debian Internal Projects"). I continuously kept on talking about this (MiniDebConf Peking 2005, DebConf 5, Helsinki (video), DebConf 7, Edinburgh (video), DebConf 8, Mar del Plata (video), DebConf 9, Cáceres (video), MiniDebConf Berlin 2010 (video in German), MiniDebConf Paris 2010 (not video recorded), DebConf 11, Banja Luka (video) ... and these are only (Mini)DebConfs my talks page is full of this topic) and every new year I try different ways to communicate the idea to my fellow Debianistas. I'm wondering how I could invent a title + abstract avoiding the term Blends, put "Git", "release" and "systemd versus upstart" in and being able to inform about Blends reasonably by not becoming to off topic with the abstract.

I also registered the Debian Science round table. I admit we were lacking some input from remote via IRC which used to be quite helpful in the past. The attendees agreed upon the handling of citations in debian/upstream files which was invented by Debian Med team to create even stronger bounds to our upstream developers by giving their work extra reward and providing users with even better documentation (see my summary in Wiki). As usual I suggested to create some Debian Science offsprings like "Debian Astronomy", "Debian Electronics", "Debian Mathematics", "Debian Physics" etc. who could perfectly leave the Debian Science umbrella to get a more fine grained structure and a more focused team to enhance the contact to our users. Unfortunately there is nobody who volunteers to take over the lead for such Blends. I have given a short summary about this BoF on the Debian Science mailing list.

In the Debian Med meeting I have given some status report. No other long term team members were attending DebConf and so I gave some kind of introduction for newcomers and interested people. I touched also the DebiChem topic which maintains some packages that are used by biologists frequently and so we have a good connection to this team.

Finally I had registered three BoFs in Blends I'm actually not (or not yet) active part of. My motivation was to turn the ideas I have explained in my main talk into specific application inside these teams and helping them to implement the Blends framework.

In the first BoF about Debian GIS I have shown the usual team metrics graphs to demonstrate, that the one packaging team Pkg-OSM is in danger to become MIA. There are only three persons doing actual uploads. Two of them were at DebConf but did not joined the BoF because they do not consider their contribution to Pkg-OSM as a major part of their general Debian work. I will contact the main contributor David Paleino about his opinion to move the packages step by step into maintenance of Debian GIS packaging team to try to overcome the split of two teams that are sharing a good amount of interest. At least if I might become an Uploader for one of the packages currently maintained by Pkg-OSM I will move this to pkg-grass-devel (which is the name of the packaging team of Debian GIS for historical reasons). The attendees of the BoF have considered this plan as sensible.

Moreover I talked about my experiences with OSGeo Live - an Ubuntu derivative that tries to provide a full tool chain to work on GIS and OSM problems ... basically the same goal as Debian GIS has just provided by the OSGeo project. I'm lurking on OSGeo mailing list when I asked explicitly I've got the answer that they are working together with Debian GIS and are using common repository (which is IMHO the optimal way of cooperation). However, it seems that several protagonists of OSGeo Live are underestimating the resources provided by Debian. For instance there was a question about Java packaging issues but people were not aware about the existence of the debian-java mailing list. I was able to give an example how the Debian Med team managed to strengthen its ties to BioLinux that is also an Ubuntu derivative for biologists. At our first Debian Med sprint in 2011 we invited developers from BioLinux and reached a state where they are using the very same VCS on Alioth where we are maintaining our packages. At DebConf I was able to upload two packages where BioLinux developers did certain changes for enhancing the user experience. My "work" was just bumping the version number in changelog and so we did profit from the work of the BioLinux developers as well as they are profiting from our work. I plan to dive a bit more into Debian GIS and try to strengthen the connection to OSGeo Live a bit.

The next BoF was the Debian Multimedia meeting. It was nice that the current leader of Ubuntu Studio Kaj Ailomaa joined the meeting. When I was explaining my ideas about cooperation with derivatives I repeated my detailed explanation about the relation with BioLinux. It seems every topic you could cover inside Debian has its related derivative. So to me it seems to be quite natural to work together with the developers of the derivative to join forces. I actually consider a Blend a derivative done the right way = inside Debian. The final work for the derivers that might be left for them is doing some shiny customising of backgrounds or something like this - but all the hard work could and should be done in common with the relevant Debian team. My dream is to raise such relevant teams inside Debian ... the Blends.

Finally the last BoF of this series was the Debian Games meeting. As always I presented the team metrics graphs and the Debian Games team members who attended the BoF were quite interested. So it seems to be some unknown fact that team metrics are done for several teams in side Debian and so I repeat the link to it for those who are not yet aware of it. As a result of the BoF Debian Games team members agreed to put some more effort into maintaining their Blends tasks. Moreover Miriam Ruiz wants to put some effort into reviving Debian Jr. Regarding Debian Jr. there was an interesting talk about DouDouLinux - in case you might want to watch the video I'd recommend skipping the first 30min and rather watch the nice live demo. There was also an ad hoc BoF about Debian Jr scheduled to bring together all people interested into this cute project and Per Anderson volunteered to take over the lead. I have given a summary about this specific BoF at the Debian Jr list.

For some other talks that I'd regard as remarkable for some reasons: I'd regard the talk "Debian-LAN" by Andreas Mundt as some hidden pearl because it did not got a lot of attention but after having seen the video I was quite impressed - specifically because it is also relevant for the Blends topic.


I also liked "Paths into Debian" by Moray Allan (and I was only able to enjoy the latter talks thanks to the great work of the video team!) because it also scratched the same topic I was concerned about in my mentoring talk. Related to this was in my opinion also "Women in Debian 2013" were we tried to find out reasons for the lack of woman compared to other projects and how to overcome this issue.

Geert hovering
 over the grass Besides the talks I will probably never forget two specific moments that make DebConf so special. One of these moments is recorded on an image that clearly needs no words - just see Geert hovering over the grass.

Another strong moment in my personal record was in the DebConf Newbies BoF "First time at DebConf" that unfortunately was not recorded but at least for this statement it would have been very great if we would have some reference better than personal memory. Aarsh Shah a GSoC student from India suddenly raised up and said: "Four months ago I was not even aware that Free Software exists. Now I'm here with so many people who are totally equal. If I will tell my mother at home that I was standing in the same queue where the Debian Project Leader was queuing up for food she will never believe me." He was totally excited about things we are regarding as normal. IMHO we should memorise moments like this that might be part of the key to success in cultures, where Debian is widely unknown and very rarely in use.

Amongst these not scheduled great moments the scheduled day trip was also a great thing. I had a really hard time to decide what tour I might join but ended up in the "long distance walking (or should I say running) group". Inspired by the "running Bubulle" who was flashing between the walking groups we went uphill with 5.4km/h which was a nice exercise. Our destination the large cliff was an exciting landscape and I guess we all enjoyed the dinner organised by the "Trout cabal". ;-)

say goodby to
 friends So I had a hard time to leave Le Camp and tried hard to make sure my memories will remain as long as possible. Keeping some signs attached to my bicycle, conserving the "Scenic Hacklab" sign for my private "scenic hacklab @ home" was one part. I also have cut some branches of the Buxus sempervirens in Le Camp and have put them in my garden at home (where I create some hedgerow from places where I spent some great time). These will probably build a great part of the hedgerow ...

Thanks for reading this longish report.

Looking forward to see you all in Germany 2015 (or earlier) Andreas.

Scenic Hacklab
 @ home

Tuesday, 5 March 2013

Debian Med sprint report (by Andreas Tille)

This is the report about my work at Debian Med sprint ten days ago in Schönberger Strand. If you are interested in Sprints in general you might be interested in work item 2. below.
  1. Wrote draft article for Indian health care magazin. If you might like to proofread the article I'd be very happy (it is not yet to late for changes.) There is also a PDF version.
  2. I have given a short talk proving the importance of sprints. The slides are basically graphs and I try to prove that sprints are a really good idea. The background knowledge is that the Debian Med team is doing sprints since 2011 and looking at all graphs you can see that this has a really positive effect. Thanks to Debian and its sponsors for supporting this kind of sprints.
  3. Packaging
    • Worked with T. Travis on flexbar and uploaded the package to new queue
    • Worked with Ch. Gille on strap-base and uploaded the package to new queue
    • Discussed strategy how to strip glam2 source from meme upstream with T. Booth. Meme upstream agreed to keep the original license of Glam2 and backport the changes from Meme source archive
    • Discussed igv packaging issues with O. Sallou who updated the package and documented some issues about its dependency goby
    • Worked together with I. Maintz on cellprofiler
    • Worked together with I. Maintz on a couple of R packages which are mostly predependencies but also one Debian Med primary target (r-cran-boolnet) was uploaded to new
  4. Discussing / chatting
    • Some chat with Ch. Steigies (Debian Games, Debian m68k, Debian Science)
    • Discussion with M. Banck about DebiChem
  5. Little bit of MoM mentoring
  6. Maintain Debian Med tasks files about newly commited packages of other sprint participants
  7. General infrastucture issues
    • Issues with machine-readable files importer into UDD
    • Try to revive PET data in UDD
    • Work on installation of future host (install needed packages, create UDD clone)
Thanks to all participants of the sprint and specifically to Steffen Möller who took over the work of organising. It was fun to meet you all and I'm even looking right now forward to the next sprint hopefully beeing able to continue the graphing of positive results of sprints in our team metrics.
We had some nice food, not so nice weather and from my perspective the only drawback was that at home there would have been perfect conditions for skiing ... but finally there are preferences. ;-)
See you at next sprint!

Wednesday, 13 February 2013

Debian Med talk at FOSDEM (by Andreas Tille)

At FOSDEM I was talking even two times about Debian Med.  The talk in the morning was attached to the FOSS for scientists track and was only a short overview about the use scientists can make from Debian Med.  As usual the slides are available from my web page.
The main talk was in the evening in the Cross Distro Devroom and it was even video recorded.
It was fun to be at FOSDEM for the first time and meet a lot of Debian people and discuss new ideas with them.

Thursday, 10 January 2013

Bits from Debian Med team (Posted by Andreas Tille)

This are the new years bits from Debian Med team. We try to make the wishes for a healthy new year becoming true with Free Software. :-)

Debian Med Bug Squashing Advent Calendar 2012

As last year the Debian Med team did some advent calendar bug squashing. The summary states 15 bugs from Debian Med scope which is less than last year but Debian Med team members also did some general bug squashing to help the Wheezy release. Finally this makes a lot of sense also for Debian Med if we can speed up the release. When counting the additional 12 RC bugs fixed in the advent calendar effort we again managed to fix more than one bug per day. Please keep on squashing RC bugs for Wheezy!

Mentoring of Month

Last year Andreas Tille started the Mentoring of Month effort to lower the entrance barrier for newcomers. There was no student for every month and not each package was uploaded at end of month but expecting such a high number of newcomers would be unrealistic anyway. So I'd like to draw some positive conclusion that we now have some newcomers friendly invited to the project and some packages uploaded or at least prepared which would not be there without the MoM project. Finally all MoM students liked the project and we will continue it in the future and would like to recommend other teams to do something similar.

Planed Debian Med sprint in Kiel

The next Debian Med sprint for real life meeting of Debian Med developers and users will happen in Kiel 23rd/24th of February. All interested people are invited to join to continue the success of the past two sprints. We are currently in the planing phase but there are just some hot topics which are workflows, licensing (specifically bug #694908), cooperation with Ubuntu and BioLinux and other things.

Metapackages targeting at Wheezy

Currently Debian Med metapackages version 1.13.2 are in unstable and once the unblock request is accepted by Debian release team this version will target at Wheezy. This means your very last chance to influence the metapackage content regarding some missing dependencies is defacto over now. Please closely observe our web sentinel in case you are interested in the work of Debian Med and tell us if packages are missing from our focus.

Kind regards and see you at Debian Med sprint