[BioCocoa-dev] BioCocoa meeting

Alexander Griekspoor a.griekspoor at nki.nl
Mon Apr 4 18:30:11 EDT 2005

Hi everybody,

Here's the news I was talking about. Robert Kehrer at Apple responded 
to our question about a WWDC2005 BioCocoa meeting with the email below.
Personally I think it's a great idea to join the BioHackathon with the 
BioCocoa team, of course as it coincides with the WWDC we can meet up 
there as well. That is, I still haven't heard about a potential 
sponsorship. I'll try to bring up that subject again if we know more 
about the BioHackathon.
I discussed this off-list with Peter already, and he would like to join 
the BioHackaThon as well. Now I would like to know a few things and ask 
you guys if the following is a good idea.
First, who would be interested to join this BioHackaThon if this were 
possible. It would be a great opportunity to really hack away with 
BioCocoa and do lots of work (starting at the WWDC already of course). 
Why would you like to join, or why wouldn't you.
Second, I propose to contact the organizers of the BioHackathon as soon 
as possible to see what the possibilities are, costs, etc. We have been 
thinking in terms of the OpenBio organization already. It might be 
(way) too early to really join, but it might be the perfect opportunity 
to introduce ourselves, discuss with those people what our and their 
options are, and meet a lot of people with lots of experience and 
attract perhaps a few enthusiastic people from this field. If you all 
agree, I can do the same thing with Peter again and send an email to 
the people mentioned by Robert Kehrer. Let's then see how things 

> Alexander,
> The Apple and the OpenBio community are planning a BioHackaThon 2005 
> to be in conjunction with the WWDC 2005.
> Plans would include:
> 1) A kick-off reception on Sunday June 5th to welcome the OpenBio 
> attendees
> 2) WWDC attendance  by as many OpenBio community luminaries as possible
> 3) A 4-5 day BioHackathon on the Apple Campus in Cupertino immediately 
> following the WWDC
> Community leaders are currently identifying the appropriate attendees 
> and seeking travel and lodging funding. I expect that key people from 
> each of the various Bio* groups would be in attendance and see no 
> reason that BioCocoa couldn't be included if that project is 
> officially part of the OpenBio community.
> The BioHackathon organizers include Susanna Lewis, Cyrus Harmon, Steve 
> Chervitz and Jason Stajich (cc'ed). You should contact them to 
> investigate the participation of the BioCocoa team.
> ---
> Robert Kehrer
> strategic alliance mgr, sciences   |   worldwide developer relations
> On Mar 13, 2005, at 5:29 AM, Alexander Griekspoor wrote:
>>  Dear Robert,
>>  It was a great pleasure to meet you during WWDC 2004 right after the
>>  ceremony of the design awards and during the science lunches. Back 
>> then
>>  you told me that I could contact you whenever I needed your help with
>>  anything related to our programs and with this mail I want to make 
>> use
>>  of this promise ;-)
>>  Right after last year's meeting I got in contact with Peter Schols 
>> from
>>  Belgium who wrote a Cocoa framework - called BioCocoa - for reading 
>> and
>>  writing biological sequences. Around the same time he made his
>>  framework open source at BioInformatics.org, and I joined his team to
>>  help further development also with the idea to use it in our apps.
>>  After some discussions I proposed to broaden the general idea behind
>>  BioCocoa to a more general Bio framework, encompassing much more than
>>  sequenceIO alone. At the last WWDC, I spoke the guy from BioPerl 
>> about this
>>  and he was enthusiastic about the idea of a BioCocoa sister back 
>> then.
>>  This was exactly the idea we had in mind, and we set out to develop
>>  this great and powerful BioCocoa framework leveraging all the good
>>  things from Cocoa. Soon after, we managed to recruit a few more
>>  enthusiastic mac bioprogrammers. It turned out that all of us were
>>  reinventing the wheel time after time again for our programs, and
>>  having a great Cocoa based foundation would not only help all of us 
>> and
>>  save us much time, it will also increase the number of bio-apps for 
>> Mac
>>  OS X!
>>  Right now, our team consists of 8 enthusiastic programmers and things
>>  are starting to look really good! The core foundation begins to take
>>  shape, and it promises very much. Take a look at our mailinglist
>>  traffic and see how much effort everyone is putting into this,
>>  impressive and fun to see.
>>  A few weeks ago I proposed on the list to organize a meeting at the
>>  next WWDC. For us it would be a week where we would not only meet 
>> each
>>  other for the first time, but also a week where we discuss the
>>  directions and future of the framework much more productively.
>>  Additionally all of us could learn about the new stuff in Tiger and 
>> see
>>  how this fits in our framework (Did I say CoreData?!!!). Such a 
>> meeting
>>  would propel our efforts tremendously. It's about this subject that
>>  Peter and I would like to ask your help and at the same time do a
>>  proposal.
>>  First the help, some of the team will go for sure to the WWDC, us 
>> included
>>  (definitely addicted ;-). Possible because we're students and hope to
>>  get a scholarship. We'll pay for our own trip and hotel costs just
>>  because we JUST NEED to be there! Except for propably one person who
>>  can't take the time off from his job, everyone would like to go, they
>>  might be able to get to San Francisco, and find a place to stay, but
>>  not everyone can afford to pay the $1600 registration fee (remember
>>  your salary back then? ;-). So our question is a simple and bold one,
>>  would it be possible for Apple to sponsor our initiative and 
>> framework
>>  development with a WWDC ticket for those who do not manage to get or
>>  meet the criteria for a student scholarship?
>>  To give you an idea about how much "sponsorship" we're talking here,
>>  this is the BioCocoa team:
>>  Peter from Belgium has applied for a scholarship
>>  Mek & Tosj from The Netherlands have applied for a scholarship
>>  Jim Balhoff from the states has applied for a scholarship
>>  Philipp Seibel from Germany has applied for a scholarship
>>  Vincent Merckx from Belgium has applied for a scholarship
>>  Then we have:
>>  Charles Parnot (the one from XGrid at stanford) from Stanford
>>  John Timmer (who developed the plugin system in 4Peaks) from NY
>>  Todd Harris (who's also part of BioPerl) from Cold Spring Harbor.
>>  The sponsorship would thus be 3-5 WWDC tickets (if we all get the
>>  scholarships of course).
>>  So what's in it for Apple? Well, Apple is advertising all over the 
>> web
>>  in the past week that (Bio)Science is one of its main markets, that
>>  Macs are big in biosciences and genomics (which they are!) and that 
>> Mac
>>  OS X can play a key role as a development platform. At the same time,
>>  one of the truly great things with respect to programming is 
>> definitely
>>  the power of Cocoa. Yet we have BioRuby, BioPerl, BioJava, but no
>>  BioCocoa! We hope to fill this gap, ideally (and this I admit is 
>> really
>>  in the future) something that will grow into a real sister/brother
>>  project under the Open Bio organisation. BioCocoa will benefit us as
>>  programmers but it will also be a major selling point for Apple to
>>  promote Mac OS X in the scientific community.
>>  Finally, in this light we would like to hear if you're interested in
>>  the following proposal. What do you think of organising a scientific
>>  meeting around BioCocoa at WWDC05 (if there are any scitech meetings 
>> of
>>  course) where we present our framework to the other scientists 
>> around?
>>  It would be a great way to interest more mac science programmers for
>>  our initiative and also a great opportunity to discuss what the needs
>>  are in this respect of scientists using the mac.
>>  You find more info on BioCocoa at:
>> http://bioinformatics.org/project/?group_id=318  (bioinformatics.org,
>>  mailinglist + CVS)
>> http://bioinformatics.org/biococoa/   (original framework)
>>  What we do plan to have before the WWDC is a website dedicated to the
>>  new version of the framework, documentation about the architecture of
>>  the BioCocoa foundation, a simple demonstration application showing
>>  what the framework can do.
>>  Looking forward to your response, and see you hopefully at WWDC 2005!
>>  On behalf of the complete BioCocoa team,
>>  Alexander Griekspoor
>>  Peter Schols.
                     ** Alexander Griekspoor **
               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
                   Tel:  + 31 20 - 512 2023
                   Fax:  + 31 20 - 512 2029
                   E-mail: a.griekspoor at nki.nl
	        AIM: mekentosj at mac.com
               Web: http://www.mekentosj.com

                  EnzymeX - To cut or not to cut

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