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BioPerl is preparing for version 1.6 release in the coming months. As part of this some restructuring and simplification of the packaging is occurring.

• Bio-Graphics has been split off into its own package back on Sourceforge to allow for a separate release schedule. It will be uploaded to CPAN as a separate package. In the future other small groups of modules will also be split off from the Core.  Eventually the Core will constitute components that will be the main parsers and data objects while less-common use cases or tightly related modules (like bioperl-network) will be released to CPAN on their own.
• Tests have been split off into smaller chunks.
• Anyone who has contributed to the code and feels their name should be included in the authors’ list needs to either add it or email the mailing list or Chris Fields.
• S endu has moved ModuleBuildBioperl and BioperlTest into Bio::Root
• Bugs are being triaged at bugzilla so if you have any opinions you can vote on the bugs in the queue.

We are pleased to announce the release of Biopython 1.49. There have been some significant changes since Biopython 1.48 was released a few months ago, which is why we initially released a beta for wider testing. Thank you to all those who tried this and reported the minor problems uncovered.

As previously announced, the big news is that Biopython now uses NumPy rather than its precursor Numeric (the original Numerical Python library).

Scheduled for Nov 19, 12:30 - 2PM PST via Conference call. Please email board@open-bio.org to receive call-in information so we will know how many callers there will be.

Agenda

Old Business

1. Approve minutes from BOSC 2008 Meeting

New Business

1. To vote on a new member to the board, Kam Dahlquist
2. Discuss leadership changes and plan how Board membership will be expanded in the next year
3. BOSC 2009: planning is underway by BOSC committee, will discuss any input needed by BoD
4. Treasurer’s financial report from summer 2008, with accounts updated to be current for
5. Any purchase or server hosting decisions
   • I put some thoughts regarding the OSC hosting offer on my talk page: User:Dag – Dag 20:34, 19 November 2008 (UTC)

Minutes

Venue: held by conference call, starting 12.30pm Pacific Time (US).

The OBF Conference call is scheduled for 12:30PM to 2PM PST on Wednesday Nov 19, 2008.  Members of the Open Bioinformatics Foundation and those interested in the decisions are invited to listen in and participate.  A brief agenda is available here.

Please email Hilmar Lapp at hlapp _AT_ gmx.net for call in number and codes if you wish to participate or listen to the discussion.  Those official members should have gotten an email via the  OBF members email list.

Agenda

• Old Business
  1. Approval of minutes from 2007
• New Business
  1. Current Board
     • Confirm past term expirations of those who did not run again for the Board.
     • What to do about the Secretary seat?
     • Some of the items on the agenda here need a legitimate vote by the Board (with prior notification and quorum satisfied). Should plan for a (presumably virtual) voting Board meeting soon afterwards.
     • How can we better ensure quorum?
  2. Voting on the board appointments
     • Kam Dalhquist has already served as a major organizer for BOSC and is interested in helping lead the OBF to achieve more outreach and education.
     • Darin London has served as BOSC chair for the past 4 years
     • Strengthen connection with O|B|J
     • Procedure for appointment of additional BOD members
  3. Financial report (Treasurer)
     • Account standing, reserves
     • 501(c)3 accounting and filing status
     • Sponsorship accounting
  4. BOSC
     • Short 2007 report (attendance, talk highlights)
     • BOSC 2008 summary (attendance, talk hightlights)
     • Should BOSC 2009 to be held in conjuction with ISMB2009?
     • Possibilities for including submitted papers for a publication.
  5. OBF Membership accounting and drive to register more members
     • Membership forms physical records
     • Members who are citizens of trade-restricted countries - legal advice, file for exemption?
     • Form doesn’t give date, need to amend
  6. OBF future directions
  7. Review of By-Laws (Parliamentarian)
     • 10-days prior notice of Board meeting requirement: need to change or have a standing Board meeting (BoF) on day 1 or 2 of BOSC
     • Not clear who elects officers - members may, but not a requirement, Directors can elect officers too. Leave as is or change?

Minutes

Location: Radisson Harbourfront, 5th floor poolside, July 18, 2008

The OBF board meeting will be held via conference call on Nov 19, from 12:30PM to 2PM PST.  Agenda items and information about participating is available on the agenda webpage. We anticipate this call primarily to manage administrative tasks for the foundation. We welcome input on including more members in the OBF leadership and helping set the direction for the foundation.

We are pleased to announce a beta release of Biopython 1.49. There are been some significant changes since Biopython 1.48 was released two months ago, which is why we are initially releasing a beta for wider testing.

As previously announced, the big news is that Biopython now uses NumPy rather than its precursor Numeric (the original Numerical Python library).

As in the previous releases, Biopython 1.49 beta supports Python 2.3, 2.4 and 2.5 but should now also work fine on Python 2.6. Please note that we intend to drop support for Python 2.3 in a couple of releases time (see previous news article).

Many of you will be aware that Python 2.6 was released a month ago (October 1st, 2008). This supports a lot of new syntax and functionality, but also deprecates some old modules (e.g. the sets module).

While Biopython 1.48 does mostly work with Python 2.6, we’ve been testing with Python 2.6 and have fixed a number of deprecations or breakages in our CVS repository. If using Biopython with Python 2.6 is important to you, please help out by testing the CVS code (which needs NumPy and not Numeric) and letting us know on the mailing list or bugzilla if we’ve missed anything.

To date, Biopython releases have relied on the original numerical python library, Numeric (used in python with “import Numeric”).  In the next release we will at last be moving to its successor, NumPy (used in python with “import numpy”).

This transition is already under way in the Biopython source code repository.  For further details, or to voice your opinion or enthusiasm, please join the Biopython Mailing List(s).

Finally, for anyone interested in the background story, the SciPy project has a page describing the history of the numerical python libraries.

We are pleased to announce the release of Biopython 1.48. Some new functionality has been added, a few bugs have been fixed, the documentation has been updated, plus several obsolete modules have been deprecated (or explicitly labelled as obsolete).

The following additional file formats are now supported in Bio.SeqIO and Bio.AlignIO:

• reading and writing “tab” format (simple tab separated)
• writing “nexus” files
• reading “pir” files (NBRF/PIR)
• basic support for writing “genbank” files (GenBank plain text)

This release also fixes some problems reading Clustal alignments (introduced in Biopython 1.46 when consolidating Bio.AlignIO and Bio.Clustalw), and some updates to the Bio.Sequencing parsers.