Newsletter:2001 Winter

(taken from email posting (O|B|F) Open Bioinformatics Foundation October 2001 Newsletter biopython.org, biojava.org, bioperl.org bioXML.org (defunct), bioCORBA.org (defunct), 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 boardATopen-bio.org

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"

Board of Directors

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)

Corporate Officers

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

Address

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:

Misc. hardware & gear needed for racking our new server systems
Getting a Sun hardware support contract for the donated systems
Purchase/renewal of domain names
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/ (editor's note, also see gallery site)

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:

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

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

Web, email listserv, DNS & FTP services
Core project(s) server with RAID for our source code and developers
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 dag@sonsorol.org.

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/
**

(editor's note, see also gallery for 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

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.

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!

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.

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.

BioXML

BioDAS

Two new efforts have been initiated recently

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 formodules, scripts, and schema for developers of MOBY-related software. CVS access will be available shortly.

BioMOBY project admin: Mark Wilkinson <mwilkinson@gene.pbi.nrc.ca>

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 <elia@ebi.ac.uk>

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:

Bioperl developers
new Bioperl users
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 <dalke@dalkescientific.com>. 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 "volunteer@open-bio.org". 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 board@open-bio.org

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 volunteer@open-bio.org

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 volunteer@open-bio.org

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 volunteer@open-bio.org

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 <dag@sonsorol.org>