Subject: FYI:[Open-Bioinformatics-Foundation] All Project Open-Bio Newsletter(long) (fwd)

From: Eugene Leitl <[email-masked]>
Date: Thu, 11 Oct 2001 17:52:29 +0200 (MET DST)

---------- Forwarded message ----------
Date: Wed, 10 Oct 2001 15:20:16 -0400 (EDT)
From: Chris Dagdigian <[email-masked]>
To: [email-masked]
Subject: [Open-Bioinformatics-Foundation] All Project Open-Bio Newsletter
    (long)

This email is being sent to every person who is subscribed to one of
the discussion or announce lists that we host. Rather than cross post
to 31 individual mailing lists we merged all the subscribers into a
unique list. This helps to keep our active volunteers from getting
many copies of the same message.

===========================================================================
              (O|B|F) Open Bioinformatics Foundation
                       N E W S L E T T E R
                          October 2001
                       http://open-bio.org

               biopython.org, biojava.org, bioperl.org
	bioXML.org, bioCORBA.org, bioDAS.org, biomoby.org, etc.
===========================================================================

Introduction

 There has been very significant progress and change within our project(s)
 and organizational ranks lately; most of these changes not been
 immediately obvious or visible on our web sites or mailing lists. This
 email message is our first attempt at what will hopefully become a
 regular update on the 'big picture' status of our projects and efforts.

 If you have comments, questions or concerns about anything in this
 newsletter you can email the Open-Bio board directly at
 <[email-masked]>

Summary of topics in today's message:

  o Organizational Status
    - Our cross-project name is now the "Open Bioinformatics Foundation"
    - O|B|F is now a non-profit corporation
    - 2001/2002 Board of Directors announced
    - Legal services provided pro bono by HellerEhrman

  o Organizational Financial Summary
    - Current funds
    - BOSC'2001 profit

  o Server and Connectivity Update

  o Current & New project briefs
    - New efforts: bioMOBY & bioSOAP

  o Upcoming Events
    - ORA Bioinformatics Technology Conference
       + BOF leaders needed ASAP
    - Open-Bio Hackathon(s)
       + Phoenix, Arizona
       + Cape Town, South Africa

  o Call for Volunteers

-------------------------------------------------------------------------
ORGANIZATIONAL STATUS & NEW LEGAL REPRESENTATION
-------------------------------------------------------------------------

 Over the past few years an informal group of volunteers and open-bio
 project leaders has self-formed to handle issue that span
 all of our current projects. Many of these new needs came about as we
 began to 'own' assets such as servers and domain names and others happened
 once we began organizing bootcamps and conferences and found
 ourselves having to sign binding legal and financial agreements. This
 group has also handled all the behind the scenes work necessary to
 keep our servers and Internet connectivity running smoothly.

 It has become obvious over the past year that this "umbrella" group
 while functional could benefit greatly from a more formal
 organizational structure.

 Long talked about it was finally decided at BOSC'2001 in Copenhagen
 that we should take the plunge and incorporate the group as a formal
 not-for-profit entity. The goals of the new organization are the same as
 before: providing administrative, financial and technical support to our
 ongoing and future projects.

 The new entity will be called the "Open Bioinformatics Foundation"

 The current Directors for 2001/2002 are as follows:

  - Ewan Birney	       (European Bioinformatics Institute)
  - Steven E. Brenner  (University of California, Berkeley)
  - Andrew Dalke       (Dalke Scientific Software, LLC )
  - Chris Dagdigian    (Blackstone Computing Inc.)
  - Hilmar Lapp	       (Novartis Research Foundation)

 The Directors have chosen corporate Officers for the following positions:

  - Ewan Birney, President & Chief Executive Officer
  - Chris Dagdigian, Treasurer & Chief Financial Officer
  - Andrew Dalke, Secretary

 A rented mailbox serves as our official corporate address:

  Open Bioinformatics Foundation
  411A Highland Avenue #318
  Davis Square
  Somerville, MA 02144
  Phone/Fax 617-250-0000 x4327

 As of October 4th 2001 the Open Bioinformatics is a not-for-profit
 company incorporated in the state of Delaware. More info and links to
 our meeting minutes and organizational bylaws will be forthcoming.

New Legal Representation for the organization

 As part of the ongoing attempts to get ourselves organized we are
 very pleased to announce that we now have top-notch legal
 assistance being provided pro-bono by the law firm HellerEhrman
 (http://www.hewm.com)

 In particular we'd like to acknowledge the assistance and guidance of
 Dan Appelman who co-chairs the IT National Practice Group at
 HellerEhrman. His attorney bio can be read online at
 http://www.hewm.com/attorneys/attorneyBio.asp?attorneyID=341

-------------------------------------------------------------------------
FINANCES
-------------------------------------------------------------------------

 Our current bank account is the same one we have been using for
 several years-- a "Small Business" account registered to "The BioPerl
 Project" held at a bank in Massachusetts, USA. After the corporation
 is fully formed it is likely that will close this account and open a new
 "Open Bioinformatics Foundation" account.

 Our current bank balance is approximately $7000 USD of which most
 is earmarked to pay for BOSC'2000 facility expenses that UCSD is very
 late in billing us for. This means that practically speaking we have less
 than $1000 USD free cash at the moment. Most if not all of that
 remaining money will be used to pay filing fees and expenses
 associated with incorporating the non-profit company.

 Sun Microsystems had provided significant financial support to offset
 BOSC'2001 expenses. We have invoiced them for the full amount but
 won't consider it 'real money' until we receive the funds.

Future expenses that we foresee:

  o Misc. hardware & gear needed for racking our new server systems
  o Getting a Sun hardware support contract for the donated systems
  o Purchase/renewal of domain names
  o Supporting hackfests & misc. activities

 Needless to say cash or hardware donations are welcome.

BOSC'2001 (Copenhagen) Financial Summary

 Despite a very successful conference in Copenhagen we had some
 significant expenses caused mainly by the requirement that we use the
 designated ISMB conference company to handle registration and AV rental
 support.

 Our goal in general with BOSC meetings is to make the registration
 fee as low as possible while trying to ensure that we don't actually
 lose any money. We have made a small profit at each of the last 2
 conferences.

BOSC'2001 (Denmark) Conference financial breakdown:

  Total number of attendees: 163

  Our fixed costs per attendee were 880 DKK per person

  Income received:
	 Academic:	57 @ 1100 DKK = 62700.00 DKK
	 Corporate:	68 @ 1400 DKK = 95200.00 DKK
	 Student:	38 @ 880  DKK = 33440.00 DKK

	 Total income: 191340.00 DKK

  Expenses:
	Meeting expenses (fixed) 158933.00 DKK
	Extra AV costs		  19582.00 DKK
	Poster stands		   2640.00 DKK
	Extra flipcharts	    594.00 DKK

	 Total expenses: 181749.00 DKK

	 BOSC'2001 PROFIT: 9591.00 DKK ($1,177.00 US Dollars)

  BOSC Pictures available at http://open-bio.org/bosc2001/bosc2001_pics/

-------------------------------------------------------------------------
SERVER & CONNECTIVITY UPDATE
-------------------------------------------------------------------------

 Our upstream provider of donated internet bandwidth is upgrading its
 internet connection through October and November. There may be
 downtime or sporadic connectivity outages as this effort
 progresses. If we need to change the IP addresses of our servers the
 downtime may last 8-24 hours as the new domain info propagates outward.

 Thanks again to Genetics Institute / Wyeth Ayerst Research we now
 have secure space in which to begin unpacking and building our new
 server hardware. A short list of the hardware we have available is as
 follows:

  o 3 Sun Netra T1000 high density rackmount servers
  o 1 Sun Netra A1000 UltraSCSI RAID array
  o 1 Cobalt Raq 4 rackmount server appliance
  o 1 VALinux 1220 high density PentiumIII rackmount server

 Our current plans are to split the multiple servers out according to task:

  1) Web, email listserv, DNS & FTP services
  2) Core project(s) server with RAID for our source code and developers
  3) anonymous CVS front-end and nightly build system

 A firewall/IDS system is being worked on as a separate project.

 We will be building, integrating and rolling out these systems in
 stages over the next several months. Expect to see a few more
 announcements and solicitations for volunteer assistance as things get
 under way.

 We need people with Solaris Admin skills to help us build, tune and
 secure the Netra servers. See the section below on "Volunteers" for
 more information or contact Chris Dagdigian directly at [email-masked].

 New hardware pictures are online. We will be updating this URL as the
 build out of our new server systems continues:

 **
 http://open-bio.org/Hardware-pics/
 **

 Some website statistics:

 Apache Server Statistics as of 2 October 2001
   Server uptime: 16 days 15 hours 11 minutes 9 seconds
   Total accesses: 146,749 - Total Traffic: 2.4 GB

 Bioperl.org Website stats
   1 Year Average:  98,172 hits/month  59,925 pageviews/month
   Sep 2001      :  62,125 hits, 874,361 KB transferred, 86 hits/hour avg

 Biojava.org Website stats
   1 Year Average: 57,475 hits/month  34,389 pageviews/month
   Sep 2001      : 66,418 hits, 2,291,842 KB transferred, 92 hits/hour avg

-------------------------------------------------------------------------
INCOMPLETE PROJECT BRIEFS & ANNOUNCEMENT OF NEW PROJECTS
-------------------------------------------------------------------------
  o Biopython

      Biopython is rapidly approaching a 1.0 release with a maturing
      sequence model, support for pathways, a new parsing framework
      (Martel), and algorithms for sequence computation and
      alignment. Currently, we are adding support for more file
      formats and implementing more algorithms.  As always, volunteers
      are welcome.  In addition to coders, we also need people to work
      on testing, documentation, and web development.

  o Biojava

     Since the 1.1 release earlier this year, the emphasis of BioJava
     development has been on improved connectivity (DAS, Ensembl), and
     better flatfile parsers (EMBL, Genbank, Blast).  In the future we
     hope to see more support for ontologies, and a more general query
     mechanism.  There is also a group interested in developing an object
     model for expression data.  All contributions are welcome, whether
     documentation, code, or suggestions.  Additional tutorials are
     always extremely welcome!

  o Biocorba

     The BioCORBA project has seen increased activity after building
     numerous prototype and production servers.  Previously, two
     standards for biological objects in CORBA existed from the
     BioCORBA project and the BSA and BSANE proposals from the LSR
     group of the OMG (http://lsr.omg.org). After the meetings held at
     ISMB 2001 in Copenhagen, Denmark (dubbed the "Tivoli Meetings") a
     compatible proposal was agreed upon which combined these two
     standards.  Work is under way in the Perl and Python camps to
     implement these standards.  There is a need for Java volunteers
     to implement a BioJava <-> BioCorba bridge in the months to come.

     The end result of these standards will allow seamless launching
     of analysis applications in perl,python,and java (even C if
     someone wants to implement the client side).  Connections to
     sequence (EMBL, NCBI)  and annotation sources (Ensembl, Flybase,
     WormBase) will allow developers to integrate data sources with
     analysis systems.  This will further simplify the establishment
     of pipelines for both small laboratories and large institutions
     which wish to rely on open-bio toolkits for their informatics needs.

     Tutorials and Full documentation are being generated as well as
     skeleton programs to serve as examples.  Opportunities for
     volunteers exists in every aspect of the project and from
     evaluating the BioCORBA/BSANE standard to writing client/server
     software to helping produce documentation and testing
     applications for portability and ease of use.

  o Bioperl

     The Bioperl project continues to expand and address more needs of
     biological researchers.  New developers and contributors to the
     mailing lists have furthered the scope of the project and seek to
     address new areas of data from microarray, phylogenetics,
     bibliographic, and annotation sources as well as integrate with
     more external applications.

     Recent work has produced modules suitable for retrieving
     sequences from online sources such as swissprot and EMBL.  One
     can also submit analysis jobs to online analysis queues such as
     NCBI's blast queue and soon we will have build access to EBI
     applab analysis through the NOVELLA CORBA interfaces.  New work
     is focusing on standardizing input and output methods to these
     application servers.

     Additional resources for local DAS servers in bioperl have been
     submitted and will be part of the next major release of bioperl.
     We expect the 1.0 release to be completed by the end of 2001 and
     will continue to be a stable platform for bioinformatics software
     development in perl.  The 0.7.2 stable release is expected to be
     released in mid November and will correct a number of small bugs
     in the 0.7.1 release.  Developer releases (0.9.x unstable series)
     will continue to be released until the 1.0 release and serve as
     snapshops of working code in the release that passes all bioperl
     tests.

  o BioXML
  o BioDAS

 Two new efforts have been initiated recently

  o BioMOBY (http://biomoby.org) ** site online **

     BioMOBY is an international group of biological data hosts,
     biological data service providers, and coders whose aim is to
     achieve a maximum amount of data interoperability between host
     institutions. The website provides an online resource for
     modules, scripts, and schema for developers of MOBY-related
     software. CVS access will be available shortly.

     BioMOBY project admin: Mark Wilkinson <[email-masked]>

  o BioSOAP (http://biosoap.org) ** future site **

     biosoap.org will aim to develop a bridge system between the core
     objects of bioperl and biojava as well as between the current
     perl-based Ensembl and the upcoming java port of it. It will
     hopefully allow such things as perl scripts running with java
     objects, as well as over-the-net object oriented programming. It
     is in its infancy, so any support, advice and suggestions will be
     most appreciated.

     BioSOAP project admin: Elia Stupka <[email-masked]>

  o biostandards.org

     We've had this domain name for a while and have done nothing with
     it. Suggestions welcome.

-------------------------------------------------------------------------
UPCOMING EVENTS
-------------------------------------------------------------------------

2-Part Open Bioinformatics Hackathon in USA and South Africa !

 This is an early sneak-peek announcement. Details will follow  from
 the actual organizers.

 O'Reilly & Associates (http://www.ora.com) and Electric Genetics
 (http://www.egenetics.com) are going to jointly hold two open-bio
 hackathons. The hackfest will start with a three-day event as part of
 the O'Reilly Bioinformatics Technology Conference in Arizona in late
 January and continue with a seven-day session in Cape Town, South
 Africa scheduled for late February. The event is invitation only and
 attendees will have all travel and accomodation expenses paid.

 This is very exiting news, more details will be announced.

Open-Bio at the O'Reilly Bioinformatics Technology Conference, Jan 2002

 Conference site:  http://conferences.oreilly.com/biocon/

 It appears that many of our project admins and developers are going
 to be attending the ORA conference in January. Ewan Birney is giving
 a keynote address and several Open Bio people are giving talks and/or
 tutorials at the conference.

 In addition to the tutorial sessions, the OBF will also have a
 conference booth in the exhibit hall and we have been invited by the
 conference staff to organize and host informal Bird Of a Feather ("BOF")
 sessions as necessary.

 We have already committed to hosting the following BOF sessions at
 the conference:

     o Bioperl developers
     o new Bioperl users
     o Biopython users & developers

 HOST YOUR OWN BOF! If you are interested in hosting/moderating a
 gathering of like-minded individuals at the conference please respond
 to Andrew Dalke <[email-masked]>. We need to know (a) who
 you are and (b) what BOF topic you propose to host.

-------------------------------------------------------------------------
CALL FOR VOLUNTEERS
-------------------------------------------------------------------------

 We always welcome volunteers and are soliciting people right now for
 the following roles and projects:

  * Volunteer Coordinator

    This person or group would be responsible for monitoring a new
    email address we are going to set up called
    "[email-masked]". The coordinators will screen & manage
    volunteer offers, match them to current projects/needs and
    otherwise help with orientation and introductions.

        Time commitment: Minimal
	How to sign up  : email [email-masked]

  * Webteam (architect & deploy a new website for us)

    The problem is simple. Our web presence sucks. We need something
    better. The task of the webteam is to come up with a plan and
    follow it through.

      Time commitment: depends; may be significant in the early stages
        How to sign up: email [email-masked]

  * Mailteam

    We use the GNU Mailman system for our mailing lists. It is a nice
    piece of software that can be almost entirely administrated via a
    web interface. Once the lists are created they are largely
    self-operating. We occasionally need an administrator to respond to
    user question, manually unsubscribe the clueless and act as
    moderators when our spam mail filters quarantine suspect
    messages.

    We are looking to set up a small group of people who monitor and
    moderate the dozens of mailing lists we have currently running.

      Time commitment: minimal
        How to sign up: email [email-masked]

  * SolarisGurus

    A significant amount of our new server hardware will run
    Solaris. We need people who are available to answer configuration
    questions, idiot check changes and help with securing each box.

      Time commitment: depends; may be significant in the early stages
        How to sign up: email [email-masked]

  * CambridgeTeam

    All of our existing and future server hardware is located in
    Cambridge, Massachusetts (subway accessible via the Red
    Line!). There may come a time where we need physical bodies to
    help rack servers or possibly transport the systems to new hosting
    facilities. We are attempting to get a sense of how many people we
    have local to the area that may be available if needed.

    Time commitment: probably zero
      How to sign up: email Chris Dagdigian <[email-masked]>

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