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
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/>](http://open-bio.org/bosc2001/bosc2001_pics/)
(editor's note, also see [gallery site](http://gallery.open-bio.org))
------------------------------------------------------------------------
## 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:
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/`](http://open-bio.org/Hardware-pics/)
`**`
(editor's note, see also [gallery](http://gallery.open-bio.org) 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>`
