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):
med-bio:
+ 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)
med-bio-dev:
+ 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
med-data:
- freediams (restructuring upstream, will be back with next release hopefully)
med-imaging:
+ imagevis3d
+ itksnap
+ odin
+ volview
med-imaging-dev:
+ python-pyxnat
med-practice:
+ 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.
Tuesday, 17 April 2012
Thursday, 15 March 2012
Bits from Debian Med team (Posted by Andreas Tille)
Hi,
in this bits:
Andreas.
in this bits:
- Debian Med Bug Squashing Advent Calendar 2011
- Anniversary of Debian Med
- Second Debian Med sprint (Southport, 27th-29th January 2012)
- Mentoring of Month (MoM)
- DDs who came to Debian because of Debian Med
- Future plans
- 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
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
- Do not let wait anybody who wants to do work.
- Newcomers are frequently shy - try to invite them kindly and patiently.
- Tell people verbosely about your project - it is astonishing how less people know and what wrong assumptions they make about your project.
Andreas.
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.
version of my agenda to the Wiki page.
- 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. - 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. - 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. - Finishing sofa-framework which needs to be updatet to new version
Nothing done on this front - Bug squashing of Debian Med team maintained packages
Two bugs fixed by new upstream version of GinkgoCADx (#657827, #648167) - If time permits work on some Beast related phylogeny packages
Uploaded phy-spread package - 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. - 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 - Working on Blends sentinel bugs overview
This was terribly blocked by non-functional fetching translations from ddtp.debian.net which is down. Caring for alternatives to at least get tasks pages updated again but no success so far. (see also item 7) above) - 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
- License checking
I was suggesting an ePetition to free Phylip and wrote a first draft for it. - Mapping Southport :-)
Added some Hotels and Restaurants to OpenStreetMap
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!
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!
Friday, 28 October 2011
New set of metapackages released (Posted by Andreas Tille)
The metapackages which are used to simplify medical applications on Debian GNU/Linux systems were updated in unstable. The most important changes are:
- New metapackage med-oncology recommending package dicompyler
- New metapackage med-rehabilitation recommending package sitplus
- Metapackage med-imaging now recommends package ginkgocadx
- Metapackage med-bio recommends several new packages (as usual)
Wednesday, 3 August 2011
Debian Med BOF @ DebConf 11 in Banja Luka (Posted by Andreas Tille)
Andreas Tille had a BOF about Debian Med at DebConf 11 in Banja Luka at 30.7.2011. The slides as well as a video record can be downloaded.
Andreas had given an overview about the current status of Debian Med. It can be stated that the project which is one out of several Debian Pure Blends had made good progress over its nine years of existence. While several applications which might be used in medical care in the wider sense (which also stretches to microbiological research) were added to Debian so that we have a count of close to 200 packages it was also stated that the existence of Debian Med itself has attracted new Developers to the Debian project. Saying this Free Software for medicine profits from the Debian distribution and Debian was able to gather new manpower because this software was included.
The following TODO items were raised in the BOF
Visibility:
Andreas had given an overview about the current status of Debian Med. It can be stated that the project which is one out of several Debian Pure Blends had made good progress over its nine years of existence. While several applications which might be used in medical care in the wider sense (which also stretches to microbiological research) were added to Debian so that we have a count of close to 200 packages it was also stated that the existence of Debian Med itself has attracted new Developers to the Debian project. Saying this Free Software for medicine profits from the Debian distribution and Debian was able to gather new manpower because this software was included.
The following TODO items were raised in the BOF
Visibility:
- Logo
- more effective use of social media to attract more users
- Work together with Debian Publicity
- Release in stable PPA and announce this
- Hospital information system VistA or at least GT.M (precondition for VistA)
- Additional practice management systems FreeMed & FreeMedForms
- Further Java packages like Jalview, Beast, Artemis (biology), mayam (medical imaging), dcm4chee (PACS server)
- radiation therapy planning Prism
Friday, 22 July 2011
2011 Codefest, BOSC and ISMB
Vienna just hosted the Codefest of the Open Bioinformatics Foundation, followed by the Bioinformatics Open Source Conference (BOSC) and the main conference Intelligent Systems in Molecular Biology (ISMB). Debian Med had a talk+poster at BOSC and somehow nobody took that down for the main conference which (for some this may be the proof for the existence of some higher might) let it hang next to the only poster by Microsoft among some 1000 or so. Hillarious. It should be noted that the Microsoft representative, Dr. Simon Mercer, seems to be a nice guy and he did not take it down either.
As a community it was nice to meet many contributors to Debian again, bringing up sweet memories also from January's sprint and Tim to volunteer organising the next one. The Codefest brought preliminary packages for GMOD's chado and jbrowse in collaboration with Scott Cain, who later at BOSC finally met with Olivier, our maintainer of gbrowse. One was also reminded of a series of nice efforts to bring microscopy and its analysis of cellular images closer to Java. And besides ImageJ this also means the need for Fiji. To bring our medical and biological users closer together, those packages have some extra importance to us. After some exchance with respective upstreams, things are getting increasingly ready for our (re)distribution. Michael from the Ensembl helpdesk had a review of the Ensembl packaging and he liked it a lot, which is good. Well, this is not too surprising, since it is maintained by Eagle Genomics - professionals in Ensembl and Cloud Computing ... and sponsors of BOSC. He also encouraged us to submit patches to remove/reduce dependencies on the long outdated version 1.2.3 of BioPerl, so it could leave the experimental section. Jim Procter sees some light towards a Debian package of Jalview. BOSC then brought a series of additional promising contacts and so did the ISMB itself. There is a strong interest from many sides to get getData into a pristine shape. With Peter Rice we have now agreed to get instructions for his EMBOSS tools, maintained by Charles, into it, starting with the classical protein sequence, motif and interaction databases. One is tempted to bring also a text based human genome in from Ensembl, but we'll see how far we get.
A major dominance throughout the Codefest and BOSC in a series of presentations had the Cloud Bio-Linux initiative. Everybody seems to like it, also in industry. It will be described in more detail in a separate post. It deserves it. When Debian approaches the best possible bioinformatics environment (what is that? and for whom?) in a bottom-up approach, Cloud Bio-Linux is top-down: bring something up that works and use Debian technologies whenever this his helpful. They will ask for money, from the government and from industry, earmarked for their bioinformatics ambitions, and from those positive vibes on the conference one tends to think the'll get some. When remembering e.g. the Dunk Tank disaster, anything like that seems rather unlikely to happen from the Debian side. But that is fine. Cloud Bio-Linux is contributing to Debian, and their contributors are feeling to be a part of Debian Med, too.
The community is possibly the most important aspect of it all. The expertise on biomedical computing collected in a single room at the Codefest and BOSC is enormous. And while there are many many many many Macs on many laps, about everyone one talks to uses Ubuntu on their
desktop/servers back home. The Debian Med's repository gives them all an opportunity to bring their expertise up into a collaborative environment and form something larger from there. Last and this year this is the cloud and what you could do with it. Next year brings complete tangible workflows, we are sure.
As a community it was nice to meet many contributors to Debian again, bringing up sweet memories also from January's sprint and Tim to volunteer organising the next one. The Codefest brought preliminary packages for GMOD's chado and jbrowse in collaboration with Scott Cain, who later at BOSC finally met with Olivier, our maintainer of gbrowse. One was also reminded of a series of nice efforts to bring microscopy and its analysis of cellular images closer to Java. And besides ImageJ this also means the need for Fiji. To bring our medical and biological users closer together, those packages have some extra importance to us. After some exchance with respective upstreams, things are getting increasingly ready for our (re)distribution. Michael from the Ensembl helpdesk had a review of the Ensembl packaging and he liked it a lot, which is good. Well, this is not too surprising, since it is maintained by Eagle Genomics - professionals in Ensembl and Cloud Computing ... and sponsors of BOSC. He also encouraged us to submit patches to remove/reduce dependencies on the long outdated version 1.2.3 of BioPerl, so it could leave the experimental section. Jim Procter sees some light towards a Debian package of Jalview. BOSC then brought a series of additional promising contacts and so did the ISMB itself. There is a strong interest from many sides to get getData into a pristine shape. With Peter Rice we have now agreed to get instructions for his EMBOSS tools, maintained by Charles, into it, starting with the classical protein sequence, motif and interaction databases. One is tempted to bring also a text based human genome in from Ensembl, but we'll see how far we get.
A major dominance throughout the Codefest and BOSC in a series of presentations had the Cloud Bio-Linux initiative. Everybody seems to like it, also in industry. It will be described in more detail in a separate post. It deserves it. When Debian approaches the best possible bioinformatics environment (what is that? and for whom?) in a bottom-up approach, Cloud Bio-Linux is top-down: bring something up that works and use Debian technologies whenever this his helpful. They will ask for money, from the government and from industry, earmarked for their bioinformatics ambitions, and from those positive vibes on the conference one tends to think the'll get some. When remembering e.g. the Dunk Tank disaster, anything like that seems rather unlikely to happen from the Debian side. But that is fine. Cloud Bio-Linux is contributing to Debian, and their contributors are feeling to be a part of Debian Med, too.
The community is possibly the most important aspect of it all. The expertise on biomedical computing collected in a single room at the Codefest and BOSC is enormous. And while there are many many many many Macs on many laps, about everyone one talks to uses Ubuntu on their
desktop/servers back home. The Debian Med's repository gives them all an opportunity to bring their expertise up into a collaborative environment and form something larger from there. Last and this year this is the cloud and what you could do with it. Next year brings complete tangible workflows, we are sure.
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