debianmed: individuals' expertise and their sharing of package build instructions (Steffen Moeller)

1. Debian Med in 2011
Steffen Möller
for the
Debian Med Community
Bioinformatics Open Source Conference
Vienna, 2011

2. The Challenge – a technical view
● Increasing specialisation of tools and databases
● Access to larger number of resources
● Frequent external updates
● Increase in local administrative work
● Project-specific installations
● Differential or Meta-analyses
● Increasing platform diversity
● Local vs cloud
● Local vs mobile

3. The Challenge – a community
perspective
● Work sharing
● Somebody somewhere has installed what you are about to install
● Packaging is tremendously helpful even when you do it just for yourself
● The distribution of such packages allows other researchers profit from your effort
● Skill sharing
● Not everyone knows how to install everything correctly
● Tutorials / Mailing list discussions shall refer to identically installed packages
● Collaborative Outreach
● Computational biologists get instant access to software packages
– Working out of the box
– Compiling out of the box
● Debian Med has professional non-scientists sending patches to the researchers

4. Science and the role of a Linux
Distribution
● Publication of findings
● World-wide distribution of methods
● Authorships and publications are forwarded in package
descriptions
● Collaboration
● Software packages “meet” in the distribution
● Availability of source code as invitation to contribute
● Education
● Reach out to students at every level
● No black boxes

5. “What is special about Debian (Med)?”
● We are not special
● active support of downstream distributions, e.g. Ubuntu
● the converse
● Debian can be you!
● open to everyone
● training “on the job” to get your packages in
● finding volunteers to maintain packages for you
● Med Community support
● shared package maintenance via subversion / git
● portal to bug reports, biological packages
● “ontology-like” tagging of packages

6. What happened since BOSC 2010
● Many new packages
NGS (qiime), Ensembl, Blast+, gbrowse
● Many updates
Autodocktools, BALLView, Bio*
● Many new contributors
● Many new users
● Bio Cloud environments using Debian
● GSoC project for “Cluster in Cloud” worked with Torque
● Basic cloud images with Debian/Ubuntu became a commodity
● Debian Med Sprint on Bioinformatics (January)
● Closed loop for packaging with NERC Bio-Linux
● Close ties with Taverna and Eagle Genomics

7. Steady increase in new users
● Showing Debian graphs from popcon.debian.org, for
Ubuntu multiply by 8
● An average package is installed more frequently than
there are participants at BOSC+ISMB together
● Separate listing of recent installations / recent use
R/qtl ~700
clustalw ~240
mafft ~240

8. Inter-institutional team building
● Maintenance by active contributor to source code
● true interest in bug reports
● barrier free talking to providers of external libraries
● immediate feedback on incompatibilities
● Community
● influx of skills with every package supported
● volunteers address the details in packaging work
– Translations
– Format changes ...
● fluent transition between power user and developer
● appeal to volunteers
– Packages can be immediately modified and rebuilt
– Students at all levels and non-scientists may contribute

9. Ongoing development
● Packaging of classical Java developments
● Taverna's build dependencies still are not all in Debian – not in the right
version, this means
● similarly for Jalview – Java is difficult because of jar files shipping with
source code
● Establishment of complete workflows
● closing gaps on tutorials
● packages missing for
– In silico docking
– Automated genome assembly and annotation
● Data management
● BioMaj – very nice GUI application
● getData – may be first to link data with Debian packages

10. “Not even source” packages
● Some tools like VMD or Rosetta are surprisingly not in Debian, even
though they allow the download of source code
● But they don't allow to redistribute anything, which is sad since these
tools are not straight-forward to compile
– Compiler version likely to be newer than expected
– Libraries like BOOST may have deprecated a function
– Source code may require patches that are only found in discussion forums
● Debian Med hence hosts only the automated build instructions
● Ironically, this “not even source” concept was first adopted by CERN,
where they have Debian packages for their particle analysis tools - in
reaction to the BOSC abstract

11. What's next
● We need those problem solving workflows running
smoothly
● Hoping to bring the Medical and Biological parts of
Debian Med closer together
● Ontologies (nothing in Debian yet, again it's Java) and
reasoning
● Phenotyping of individuals and respective data
management
● Finding more bioinformatics groups already using
Debian (or its derivatives) to help reducing
redundancies and work with us all

12. Visit Debian Med on
http://debian-med.alioth.debian.org
http://wiki.debian.org/DebianMed
or just use Debian, Ubuntu or any of its derived
distributions
at home or work
directly, virtually or in the cloud