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

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  1. 1. Debian Med in 2011 Steffen Möller for the Debian Med CommunityBioinformatics Open Source Conference Vienna, 2011
  2. 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. 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. 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. 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. 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. 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. 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. 9. Ongoing development● Packaging of classical Java developments ● Tavernas 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. 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 dont 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. 11. Whats 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 its 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. 12. Visit Debian Med onhttp://debian-med.alioth.debian.orghttp://wiki.debian.org/DebianMedor just use Debian, Ubuntu or any of its deriveddistributions at home or work directly, virtually or in the cloud