Retreats Fall2012

Fall 2012, 16.9. - 18.9. September Tübingen

General Agenda Items

• replace old/inactive Maintainers, maybe find new ones? Is the maintainer concept even working?
• how to integrate code from Zurich => either utilities or tools (tested and general usefulness)
• reimplement a mapaligner and featurelinker (inlcuding feature linker functionality)
• go through all the TRAC tickets: discuss their relevance - propose solutions, prioritize
• Workflows
  • KNIME overview
  • Changes in CTD format, relationship to other packages (GKN, SEQAN, BALL)
  • Schedule for the transition from TOPPAS to KNIME
  • TOPPAS wf exporter
  • Integration of KNIME packages into nightly builds
• capsuling vs. interface redesign (ticket #184 (and #448))
• introduce "Require" statements into algorithms, e.g. consensusID requires an IDPEP preprocessing for scores, warn or error otherwise.
• Use of boost in OpenMS
• File formats: mzTab quant & qcML
• Start/discuss the planing for OpenMS 2.0, see the [wiki:OpenMS2.0Planing OpenMS 2.0 planing page], here we only list a subset of topics to give an overview
  • restructure KERNEL
  • GSL removal
  • Licences change -> BSD-3-clause, update LICENSE and AUTHORS file (see also http://www.harmonyagreements.org/index.html)
  • change file headers according to licenses change
  • Do we need the contrib for linux/mac? (at least a more concise documentation regarding potential seg.fault sources, e.g. when a (other version of a) contrib lib is already installed on OS, fix at install is another possibility)
• Finalize OpenMS 1.10 release before User Meeting
• cv-term usage (#387)
• mascot adaptors
• OMSSA: produces two top-rankings for peptides with L/I
• python/cython support (changes in build system)
  • Uwe Schmitt from Saarbrücken will introduce his plans for that
  • prioritize classes for the wrapping
  • discuss unit testing concept, tests for consistency of C++ and python classes
  • pythonic vs. identical interfaces
  • integration into build system
  • python TOPP node?
• Finalize R interface/TOPP tool
• Change of code hosting platform (Hosted Apps Retirement)
• tolerances in ppm (#39)
• rethink visualisation
  • future role of TOPPView
  • interface to Scaffold?

Detailed Agenda

Sunday

Arrival Berlin Team, dinner * Licences change -> BSD (!) * GSL removal Preliminary discussions: * rethink visualisation * moore boost in OpenMS ;) * capsuling vs. interface redesingn (ticket #184 (and #448))

Monday

TOPs: Morning

• go through all the TRAC tickets: discuss their relevance - propose solutions
• revamp mapaligner and featurelinker => Poseclustering revamped by Chris => interface change pending : Hendrik, Stephan, Oliver, Chris, Hannes J.
• introduce index part in mzML files
• replace old/inactive Maintainers, maybe find new ones? Is the maintainer concept even working?
• introduce "Require" statements into algorithms, e.g. consensusID requires an IDPEP preprocessing for scores, warn or error otherwise.
• GSL removal (replace with what? Eigen? ZIB Software?) => Erhan, Timo (Boost can replace random numbers, Eigen can do fitters, remaining are various splines (maybe not all?) )
• change file headers according to licenses change (Hendrik und Stephan)
• Sourceforge/Trac ? => We stay until we know what will happen at sourceforge
• Rework the website: => Knut, Oliver
  • reflect changes in license
  • update team pages
  • developer group photo

afternoon

• knime workflows
• correct CTD writeout for some TOPPtools (see Attachment) (Stephan Aiche is the CTD guardian)
• TOOLS vs UTILITIES
  • clean up the two directories, deprecations?
  • determine TOOL/UTILITY status for some of them (MS simulator?, SuperHirn2?)
  • testing of tools vs. utilities, inclusion in WF systems
• python/Cython (Uwe makes special branch. Will not be in 1.10 (maybe in 1.10.1), can be activated via compile, offers python support for core data structures)
• interfacing with R (build system) (Marc, Erhan)
• cv-term usage (#387)

Evening

• Start preparations for the upcoming OpenMS 1.10 release and finalize release schedule (release in October/November) (Manager/GK: Timo und Erhan)

Tuesday

• remaining TOPs from Monday
• Start/discuss the planing for OpenMS 2.0, see the [wiki:OpenMS2.0Planing OpenMS 2.0 planing page], here we only list a subset of topics to give an overview
  • restructure KERNEL
  • Do we need the contrib for linux/mac? (at least a more concise documentation regarding potential seg.fault sources, e.g. when a (other version of a) contrib lib is already installed on OS, fix at install is another possibility)
• mascot adaptors
• OMSSA: produces two top-rankings for peptides with L/I
• Fileformats: MzTab quant & qcML, experiment identifier in mzIdentML for tracking origin of ids after merge
• tolerances in ppm (#39)
• rethink visualisation