[Open-Bioinformatics-Foundation] All Project Open-Bio Newsletter (long)
Chris Dagdigian
dag@sonsorol.org
Wed, 10 Oct 2001 15:20:16 -0400 (EDT)
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
<board@open-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"
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 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/
**
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 <mwilkinson@gene.pbi.nrc.ca>
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 <elia@ebi.ac.uk>
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 <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>