[Bioperl-l] BOSC take home msgs

[Jason Stajich]

Just to give a heads up for those not at BOSC and the Bioperl BoF

Here are the take home messages:

- There is an interest from several companies using Bioperl in-house, for
  a pay-for-service consultants to help them get up to speed and fully
  realize bioperl's capabilities.  This is likely everything from
  education to troubleshooting to systems design to technical support.

  To solve this I think the OBF would be willing to be a referral service
  for consultants supporting open source bioinformatics software.  We have
  to set up the logistics on our side which would include a few email
  aliases, will send a note when this gets done.  If you have feedback on
  this idea let us know.

- Martin has proposed Bio::AnalysisFactory - perhaps to be named
  Bio::Tools::Run::AnalysisFactory - which will be where we will try and
  aggregate a general factory for running analyses either at local or
  remote hosts.  This will provide a transparent connection for the Pise,
  Novella, local apps, and other analsysis queues.

  This will be part of his Novella bridge and likely a refactoring of the
  way that Bio::Factory::EMBOSS is written - moving that to bioperl-run
  cvs module.

- The mailing archives list should be searchable with a real local search
  engine.  I've proposed ht://dig which should be reasonably easy to
  setup.  I'll feel better about this in terms of disk space once we move
  the CVS repository and all the user accounts to the new dev box which
  has lots of disk space.

- A set of HOWTOs will be written, don't have the list of who
  volunteered with me right now but these are to go into doc/howto.  For
  those who want to write in SGML/Docbook you can put yours in
  doc/howto/sgml and render the txt version in the dir above.
  Sue will oversee testing these that they work and are correct as far as
  she can.  Readability is a plus too!

  These are documents that should be designate either as for a user
  or for a developer.  Do not try and do both.    If you have ideas
  about interesting stories where you have used Bioperl to solve a
  problem, or want to write a narrative of your interpretation of how to
  use the objects in various situations this is the place.

- Objects to handle expression objects have been suggested by a couple of
  different groups.  Typically expression handling is quite specific to
  what a particular lab is doing so we may do a few iterations of
  development on these modules to make them general enough for public
  consuption.  We hope that people who have promised to submit their
  modules will follow through as it will be very useful to have an
  initial set of objects.

- Supporting Windows users.  None of the Bioperl core use windows for
  their informatics work so are really not the best people to insure that
  things work and/or are easy on Windows.  Todd Richmond has agreed to
  write an install document.  I would like to suggest we create an
  INSTALL.windows in the bioperl root directory to help point people in
  the right diretion.  Greg Elay and others have also volunteered to help
  maintain/test the ActiveState PPD system so that we can be sure it
  works.

- The scripts/examples directory need to get a good overhaul, cataloged,
  and those that use old APIs need to get chunked or put in a broken
  directory.



-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu