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The "DebianMed/Meeting/Southport2012" page has been changed by TimBooth: http://wiki.debian.org/DebianMed/Meeting/Southport2012?action=diff&rev1=82&rev2=83 Comment: added outcomes for the meeting = Debian Med sprint meeting in Southport = - After the success of the last [[DebianMed/Meeting/Luebeck2011|Debian Med sprint meeting in Lübeck]] we were granted the opportunity to organise a similar event in early 2012. This page assists in planning the event and records outcomes of the meeting. + After the success of the last [[DebianMed/Meeting/Luebeck2011|Debian Med sprint meeting in Lübeck]] we were granted the opportunity to organise a similar event in early 2012. This page is here to assist in planning the event and recording outcomes of the meeting. - The main organiser is Tim Booth (tbooth_ceh.ac.uk), the lead NEBC Bio-Linux developer. + The main organiser was Tim Booth (tbooth_ceh.ac.uk), the lead NEBC Bio-Linux developer. == Sponsorship == || We would like to thank Sci``Engines for providing the FPGA tutorial on the Friday || We would like to thank Eucalyptus for sponsoring dinner on Saturday night || ||<:> [[http://sciengines.com|{{http://www.sciengines.com/templates/rhuk_milkyway/images/sciengines/sciengines_logo.jpg}}]] ||<:> [[http://eucalyptus.com|{{http://www.eucalyptus.com/sites/all/img/logos/eucalyptus-300x32.png}}]] || + + == Report on outcomes == + + The meeting was always intended to follow a loose agenda, taking some initial talks and topics as a starting point for the day then moving to working in small groups. At the end of each day attendees were asked to report their progress to the group. As the meeting organiser I (Tim) have digested and summarised these reports to produce a list of highlights. Also see the original agenda and Andreas' personal highlights below. + + ==== Talks and group sessions ==== + + * The Sci``Engines tutorial and Friday evening ice-breaking talks went ahead as planned - see the original schedule. [I'll try and collect some slides here]. + + * On Saturday we started with a talk from Andreas on the history and structure of the Debian Med project and Debian in general. This was followed by a Q&A session. + + * On Sunday Brian started the day with a presentation on Eucalyptus, their software architecture and company strategy. + + ==== Topics and outputs of group working ==== + + * Networking, increasing participation + * All attendees agreed this was an excellent environment for networking, asking questions, and discussing projects and ideas + * GPG keys were signed for several new developers - this was co-ordinated by Steffen (Ivo, Sascha S, Martin, others) + * Discussion of systems biology requirements and future planning. Finding sys bio workflows in myExperiment (Steffen, Laszo, Alan, Ivo) + * Created account on Launchpad, joined Deb Med PPA (Sascha S, others) + * Discussion of cloud computing following Eucalyptus talk (Brian, others) + + * Software evaluation + * Clinical relevance - evaluating tools for molecular mimicry, emergency annotation of emerging pathogens (Steffen, Matus, ...) + * Taverna exposition and evaluation (Alan, others) + * Looked at Steffens GSOC project (by Dominique Belhachemi) - relates to making EMIs (Eucalyptus images) of Deb Med (Tony) + * Looked at turning PredictProtein into a web service. Decided on how to proceed. (Laszlo, Matus) + * Looked at packaging RAILS app and Ruby gems in general - discovered impracticalities. Requires further investigation and will ask on Ruby list. (Stuart) + * Looked at Qiime unit tests - how they should be applied to the existing package (Soon, Tony) + * Discussion of getData + BioMaj and possible steps towards compatibility; uses of these tools for Galaxy packaging; publication??; integration with existing packages. Considered the possibility of getting database info from NAR - towards a "semantic" NAR database catalogue. (Steffen, Olivier, Tim, Alan, Laszlo) + * Looked at packaging OMERO for open microscopy. Contains over 800 binary .jar files so this is a major undertaking. Put a message on OMERO community support board asking for a source tarball for each release. (Tony, Andreas, Tim) + * Investigated Maven debian helpers - determined that they need work (Stuart, Tim) + * Looked at issues with packaging API key to Bioportal - decided to query this with site maintainers (Stuart) + * Looked at issues with packaging Seek - maybe a scripted install is appropriate (Stuart) + + * New packages, package uploads + * Upload of Phy-Spread package (Andreas) + * Dependency packaging for BEAST - which is a mess (Andreas, Olivier) + * Work on Beast-mcmc but this is a mess (Andreas) + * CHADO (from GMOD) packaging and sponsoring into Debian, including fixes to satisfy Debian policy (Andreas, Olivier) + * PyHMM packaged (Piero, Tim) + * PSCoils packaging and improvement of code to fix Debian compatibility - demonstrating how useful it is to involve upstream authros directly in packaging (Piero) + * prdcchmm packaging - depended on PyHMM (Piero, Andreas) + * TreeVector initial packaging (Brian) + * Initial Rightfield packaging - Java app with awkward dependencies but good progress was made and a working package now exists (Alan, Stuart, Quyen, Tim) + * Packaging of Copasi (Ivo) + * libsbml update in progress (Ivo) + * Initial packaging of Genometools - mainly modifying Makefiles to make things less self contained, build dynamic libs, etc. (Sascha S, Steffen) + * Packaging CSnake which is the build system for Gimias. Almost finished. Patches ready to push to upstream (Martin, Tim) + * Started PredictProtein packaging implementation (Laszlo, Matus) + * Ensembl packaging work on libwww-perl (Andreas) + * sofa-framework update (Andreas) + * uploaded phy-spread package (Andreas) + * MMTK packaging work (Olivier) + * CLapack packaging work (Olivier) + + * Mentoring, tutorials + * Demonstration of packaging from scratch (PyHMM) on overhead projector (Tim, to Piero + many others) + * Mentoring of Mom (mentoring of the month) student (Andreas) + * Introduction to SVN usage for new contributors (Steffen to Brian) + * Demonstration of BioMaj software (Olivier to Laszlo etc.) + * Discussion of practical ways to expose software as Taverna service (Alan to Laszlo etc.) + * Demonstration of Java packaging and use of the auto-patch feature of dpkg-source (Brian) + * Sascha S received advice on how to split up a large package (genometools) into six components. Did some modifications to upstream (as the owner) to use standard file locations. Looked into licensing - issues are ongoing but generally looks good + * New prospective packagers ran through on-line tutorial to get initial hands-on experience (Quyen etc.) + + * Advocacy, licensing issues + * General discussion of DFSG and what it means for companies like Sci``Engines (Sascha M, Daniel, etc.) + * Review of "nearly free" software (eg. Phylip) leading to discussion on DFSG and legal issues relating specifically to UW and FHCRC software releases - should we have an on-line petition? (all attendees) + * Petition started to reform Phylip license (Andreas) + * Looking at BLIMPS licensing. Soon needs sift which depends on BLIMPS (abandoned). Both have nearly-free license. (Laszlo, Soon) + * CHADO promotion planning now that the package is ready (Steffen, Olivier) + == Location/Date/Capacity == @@ -78, +151 @@ ||14|| Quyen Nguyen || pre.sur_h-its.org || HITS (Seek) || Heidelberg (D) || Friday || Monday || confirmed 14/12 || From Manchester with Alan+Stuart || ||15|| Martin Steghöfer || msteghofer_cistib.upf.edu || CISTIB/Gimias (workflows) || Barcelona (E) || Fri 27.01.12 || Sun 29.01.12 || confirmed 18/1/12 || || ||16|| Matus Kalas || pre.sur_bccs.uib.no|| U Bergen (BioXSD, EDAM) || Bergen (N) || Thu || Sun morning || confirmed 11/1/12 || || - ||17|| Stefan Baumgart || presur_sciengines.com || SciEngines || Kiel (D) || Thu || Sun || confirmed 20/1 || Staying at Carlton House || + ||17|| Sascha Moeller || presur_sciengines.com || SciEngines || Kiel (D) || Thu || Sun || confirmed 20/1 || Staying at Carlton House || ||18|| Daniel Siebert || || SciEngines || Kiel (D) || Thu || Sun || confirmed 20/1 || Staying at Carlton House || - ||19|| William Spooner || [email protected] || Eagle Genomics || Babraham (UK) || Fri || Mon || confirmed 9/1/12 || Staying at Rosedale. May have to cancel at last minute due to deadline || + ||19|| William Spooner || [email protected] || Eagle Genomics || Babraham (UK) || Fri || Mon || confirmed 9/1/12 || Staying at Rosedale. Had to cancel at last minute due to deadline || - ||20|| Jim Procter || jsur_compbio.dundee.ac.uk || U Dundee (Jalview,java in debian, osgi) || Dundee (UK) || Cancelled || Cancelled || Cancelled || Dundee || + ||20|| Jim Procter || jsur_compbio.dundee.ac.uk || U Dundee (Jalview,java in debian, osgi) || Dundee (UK) || Cancelled || Cancelled || Cancelled || Had to cancel at last minute due to deadline || == Agenda == @@ -174, +247 @@ == Related meetings == + We hope that after two successful meetings this event will continue in subsequent years. + It's worth noting for those not in the know that there is some symbiosis between this sprint event and the annual [[http://www.open-bio.org/wiki/Codefest_2011|BOSC Codefest]] which is held before the [[http://www.iscb.org/ismbeccb2011|ISMB conference]]. Though the meetings are quite different in focus, they have recently engaged many of the same people and projects. == See also == _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
