[BioCocoa-dev] BioCocoa meeting
Koen van der Drift
kvddrift at earthlink.net
Mon Apr 4 18:44:51 EDT 2005
Great news Alex,
I guess I need to find a new job with more vacation days :D
On Apr 4, 2005, at 6:30 PM, Alexander Griekspoor wrote:
> 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
> 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 evolve....
>> 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
>> 2) WWDC attendance by as many OpenBio community luminaries as
>> 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
>>> you told me that I could contact you whenever I needed your help
>>> anything related to our programs and with this mail I want to make
>>> of this promise ;-)
>>> Right after last year's meeting I got in contact with Peter Schols
>>> Belgium who wrote a Cocoa framework - called BioCocoa - for reading
>>> writing biological sequences. Around the same time he made his
>>> framework open source at BioInformatics.org, and I joined his team
>>> 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
>>> 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
>>> 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
>>> save us much time, it will also increase the number of bio-apps for
>>> OS X!
>>> Right now, our team consists of 8 enthusiastic programmers and
>>> 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
>>> 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
>>> how this fits in our framework (Did I say CoreData?!!!). Such a
>>> 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
>>> First the help, some of the team will go for sure to the WWDC, us
>>> (definitely addicted ;-). Possible because we're students and hope
>>> 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,
>>> 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
>>> would it be possible for Apple to sponsor our initiative and
>>> 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
>>> 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
>>> OS X can play a key role as a development platform. At the same
>>> one of the truly great things with respect to programming is
>>> 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
>>> 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
>>> It would be a great way to interest more mac science programmers for
>>> our initiative and also a great opportunity to discuss what the
>>> 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
>>> new version of the framework, documentation about the architecture
>>> the BioCocoa foundation, a simple demonstration application showing
>>> what the framework can do.
>>> Looking forward to your response, and see you hopefully at WWDC
>>> 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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