[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

- Koen.

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 
> 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 evolve....
> Cheers,
> Alex
>> 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
>              http://www.mekentosj.com/enzymex
> *********************************************************
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