Sunday 15 July 2012

Debian Med Bits: Report from LSM Geneva by Andreas Tille

In this report from LSM 2012 in Geneva I will report about
  1. Medical imaging using Debian
  2. Debian Med packaging workshop
  3. Integration of VistA into Debian
  4. Other interesting talks

Medical imaging using Debian

There were about 10 attendees basically upstream developers of medical imaging software.  The talk got some attention and the message to include even more medical imaging software into Debian was well percived.  Thanks to Mathieu Malaterre there was some live demonstration which was way easier for him as a medical imaging expert than it would have been for me.

Debian Med packaging workshop

Due to my advertising in the talk yesterday three students (two of them from one medical imaging project, one from an other project) attended the workshop.  Thanks to Axel Beckert who helped me out surviving the challenge to walk on unexplored ground.

The idea of the workshop was to ask the attendees to name a package of their own and just package this.  Because two of the attendees were upstream developers of CreaTools we decided to go on for packaging this.  After circumeventing some pitfalls in the beginning it went rather smoothly and after about 2.5 hours we were able to commit some initial packaging to the Debian Med Git repository which comes quite close to a ready package (perhaps some split into a library and a development package needs to be done and for sure testing is needed).
Quoting Frederic Cervenansky, upstream of CreaTools
Thanks for your work. Your workshop was very interesting and didactic: a relevant discussion between Claire and me for the future of Creatools has emerged from the difficulties you  encountered to package creatools. I will try, before the end of the month, to fully package creatools. And for sure, I will contact the debian-med mailing list.

Integration of VistA into Debian

I had the good chance to directly address some issues of Claudio Zaugg the speaker in the talk Implementing open source Health Information Systems in Low- and Middle Income Countries – a practical review directly before mine.  It turned out that by using Debian packaged software might help simplifying the issues they had in supporting health care workers in Low- and Middle Income Countries.
My talk was partly repeating some basic ideas about Debian Med from the talk on Monday because the audience was completely different.  Than I tried to explain in detail how we tried hard to establish good contacts to upstream developers and why this is essential to finalise the goal to include hospital information systems straight into Debian any by doing so open the doors of hospitals for large scale Debian installations.
There is also video recording of this talk.

Other interesting talks

OpenEMR, a multi-language free open source electronic health record for international use

Just discussed the packaging of OpenEMR which is prepared for Debian Med as it can be seen on our tasks page.  The contact to the creator of some inofficial package will be established to finalise this task.

OpenFovea : when open-source and biophysical research get married

Just another target for Debian Med popped up in this talk to further enhance Debian Med in covering all issues of medical care on one hand and on the other hand helping upstream authors to distribute their code
more effectively.

Collaborative software development for nanoscale physics

The talk would have fit very nicely into the Debian Science workshop at ESRF (European Synchrotron Radiation Facility) in Grenoble because it was about ETRF (European Theoretical Radiation Facility).  At previous LSM events I had just talked with Yann and the work to include their software into Debian is on its way.

Free software and High Performance Computing

This talk was not directly connected to my Debian work but I simply enjoyed to see how "two people" had a really entertaining talk about Top 500 computers.  Vittoria, you made my last day at LSM.

Tuesday 17 April 2012

New Debian Med metapackages uploaded (Posted by Andreas Tille)

I just uploaded new metapackages featuring dependencies of several new packages prepared thanks to the great work of the Debian Med team. Here are the newcomers (and packages we lost):

+ ballview
+ bowtie2
+ cd-hit
+ clustalo
+ ffindex
+ gassst
+ grinder
+ hhsuite
+ profphd-utils
+ proftmb
+ profphd
+ profphd-utils
+ pynast
+ qiime
+ r-bioc-cummerbund
+ reprof
- seq-gen (turned out to be non-free)

+ libchado-perl
+ libffindex0-dev
+ libtfbs-perl
+ libpal-java
+ librg-reprof-bundle-perl
+ librostlab-blast0-dev
+ librostlab-blast-doc
+ librostlab3-dev
+ librostlab-doc
+ libzerg0-dev
+ libzerg-perl

- freediams (restructuring upstream, will be back with next release hopefully)

+ imagevis3d
+ itksnap
+ odin
+ volview

+ python-pyxnat

+ clinica
- freediams (restructuring upstream, will be back with next release hopefully)

Seems the regular sprints of the Debian Med team have enhanced the team (regarding the number of people and the effectivity of the cooperation). Thanks to all people who joined our effort to make Debian the best free operating system for medical care and biological research.

Thursday 15 March 2012

Bits from Debian Med team (Posted by Andreas Tille)


in this bits:
  1. Debian Med Bug Squashing Advent Calendar 2011
  2. Anniversary of Debian Med
  3. Second Debian Med sprint (Southport, 27th-29th January 2012)
  4. Mentoring of Month (MoM)
  5. DDs who came to Debian because of Debian Med
  6. Future plans
  7. General lessons learned

Debian Med Bug Squashing Advent Calendar 2011

In December last year Thorsten Alteholz has started a nice QA initiative which might be interesting for other teams next Advent. The Debian Med team was able to fix about 70 bugs in this time. Thanks to Thorsten for this nice piece of motivation and thanks to everybody who took part in the bug squashing.

Anniversary of Debian Med

On Mon, 7 Jan 2002 the Debian Med project was first officially announced. I submitted a short blog posting about this and perhaps you might like to see a long sequence of talks about this topic.

Second Debian Med sprint (Southport, 27th-29th January 2012)

In end of January 2012 the Debian Med team has met to the second sprint. As last year I would call this a very successfull event and I would recommend other teams to instanciate such meetings as well. Feel free to read my more verbose report.

Mentoring of Month (MoM)

I have started this project for the following reasons:
  • gather more manpower to the team
  • strengthen connections to upstream (which might become MoM students)
  • help shy people to become more verbose
  • to learn myself about potential problems of people who do not feel fit for packaging tasks

I made a short summary how the first MoM project worked (see at bottom).

DDs who came to Debian because of Debian Med

After realising that several members of the Debian Med team finally became DDs I made a little survey to find out about their reasons to become DD / DM. I came to the conclusion that a Blend could be a nice entry point for people to join Debian because newcomers can identify themselves with a known topic (the scope of the Blend - in this case medicine and bioinformatics) first and learn Debian rules in a team with common interest. This perfectly fits my expectation which I had from the beginning 10 years ago and I would be very happy if other Blends would follow this example to be nice, inviting and try to *actively* ask people for cooperation (see some simple rules which I learned in this process below). In the teammetrics GSOC project some graphs were created where you can see the level of contribution of these people (and other team members).

Future plans

Currently some heavy work regarding bringing bibliographic references about packages straight into package information is going on. This topic is specifically interesting in Biology because programs are frequently connected to some publication about the methods used inside the code. This topic is as well relevant to Debian Science and DebiChem. Thanks to the patient work done by Charles Plessy we now have about 70 packages featuring debian/upstream files featuring bibliographic references and there is ongoing work to move these data to UDD to enable further usage. We are in the process of final polishing the format and finishing scripts for the import. If people are interested to join this effort this would be the right moment to raise their hand.

General lessons learned

  1. Do not let wait anybody who wants to do work.
  2. Newcomers are frequently shy - try to invite them kindly and patiently.
  3. Tell people verbosely about your project - it is astonishing how less people know and what wrong assumptions they make about your project.

Kind regards

Wednesday 1 February 2012

Report from Debian Med sprint (Posted by Andreas Tille)

The Debian Med team has organised its second sprint in Southport last weekend. This is a report from my personal perspective. I added a short
version of my agenda
to the Wiki page.

  1. Ensembl packaging specifically working on installation in unstable without any conflicts (=trying to solve libwww issue)
    One main item for this meeting on my agenda was fixing the Ensembl package to finally enable a migration from experimental to unstable. One of the big showstopers is #636923. However, unfortunately the to persons who I urgently needed to discuss this topic did finally not attend and I was only able to determine, that the problem can be stripped down to the problematic package is actually liblwp-parallel-perl. I'll try to keep on working on this.

  2. The Beast-mcmc finishing
    This package is on my agenda since about one year and I was able to iron out nearly all included binary JAR files. However I get struck on the last problematic JAR mtj.jar is a mess of other included JARs based on f2j blas/arbapck JARs. I reached a state where I got a hint from upstream to the sources for the last JAR in this chain and I need to see whether I will be able to compile. I'll give this a try in the next couple of weeks if not I will push the package to non-free first and leave the final freeing to some later point in
    time. As usual, any help is welcome.

  3. Continuing with current MoM; presenting MoM to the audience to gather more potential students
    I kept on mentoring the student and there is further progress with the package we are focussing on. Moreover it might be that some participants from the workshop might step in for later Monthes.

  4. Finishing sofa-framework which needs to be updatet to new version
    Nothing done on this front

  5. Bug squashing of Debian Med team maintained packages
    Two bugs fixed by new upstream version of GinkgoCADx (#657827, #648167)

  6. If time permits work on some Beast related phylogeny packages
    Uploaded phy-spread package

  7. Checking status of Debian Med tasks
    The attempt to check the tasks was completely spoiled when noticing that the tools are broken because of technical changes in Debian infrastructure. Sorting this out and enabling regularly updated tasks pages is now on highest position in my priority list.

  8. Spontaneous mentoring of people
    I gave a spontaneous introductional talk about Debian and Blends structure Moreover I was mentoring Quyen, Laszlo (see list of attendees) and others about gpg keys

  9. Working on Blends sentinel bugs overview
    This was terribly blocked by non-functional fetching translations from which is down. Caring for alternatives to at least get tasks pages updated again but no success so far. (see also item 7) above)

  10. Helping others packaging and sponsoring
    • Sponsored chado (gmod suite) prepared by Olivier Sallou
    • Helped Charles Plessy getting snappy-java using Debian packaged library
    • Worked with Ivo Maintz on copasi
    • Helped Martin Steghöfer with Python packaging
    • Dived a bit into a Ruby package together with Quyen Nguyen with no certain outcome - needs further negotiation with Quyen and other upstream how to proceed
    • Checking the work of Piero Fariselli on three Python packages
    • Had a look with Toni into OpenMicroscopy noticing that it is a beast containing >100 binary JAR files inside the source and will take a talented and very patient Java expert to cope with all this stuff The good news is that upstream was quite supportive to provide a downloadable versioned archive which simplifies obtaining the source Needs (a lot) of further work which I'm unable to do myself

  11. License checking
    I was suggesting an ePetition to free Phylip and wrote a first draft for it.

  12. Mapping Southport :-)
    Added some Hotels and Restaurants to OpenStreetMap
Thanks to al participants who joined the workshop and made it a success (again). Looking foreward to next Debian Med workshop.

Also thanks to EagleGenomics for sponsering my travel expenses.

Saturday 7 January 2012

10. anniversary of Debian Med (Posted by Andreas Tille)

I'm happy to announce that the Debian Med project celebrates its 10. anniversary which was announced first at Mon, 7 Jan 2002. I propose to do a small celebration at the Debian Med sprint at end of January in Southport.
I would like to say thanks to everybody who helped the project developing from a single person with a crazy idea who started by picking
up some orphaned biomedical packages to a strong team maintaining a set of over 200 highly specialised packages with a high quality standard. Many thanks - ten years ago I did not imagine that we could reach that a strong state!