[Biococoa-dev] WWDC 2005 BioCocoa meeting

Peter Schols peter.schols at bio.kuleuven.be
Mon May 30 16:09:46 EDT 2005

Hi Charles,

Great to see you back on the list with some very interesting  
suggestions for the WWDC session.

> One thing that came to my mind first was that maybe we need to  
> define what the BioCocoa framework could be used for. Give some  
> very real examples, in particular the applications that some of you  
> guys are developing. My own personal virtual pet project would be a  
> general sequence editing program à-la DNA Strider... Maybe other  
> people at the WWDC have projects and ideas in mind. Introduction to  
> the talk could be about that: examples of potential and existing  
> applications, and how BioCocoa can speed up the development and  
> provide an open and consistent interface.

I already discussed this with Alex off-list: I'm working on classes  
to run a BLAST query. I need them for one of my own projects but I  
was planning to donate them to BioCocoa. They are still very much  
work in progress, but now that we have a BioCocoa session at the  
WWDC, I decided it might be useful and fun to demonstrate the  
functionality of these classes in a short demo during the BC session.  
So today, I cleaned the code and I put together a very simple GUI app  
that enables the user to enter a query string (a DNA sequence) and  
lists all BLAST hits in a table. The app itself is only a few lines  
of code (not counting the code in the BCBlastQuery and BCBlastResult  
classes which are not yet part of the framework but will be sometime  
in the future ;-))

> About the public interface, we could define what we want the  
> framework to provide to the users:
> - first and all: this is meant to be a COCOA framework, that will  
> strictly follow the conventions of the rest of Cocoa; after all,  
> this is the whole point if we don't want to be just "yet another  
> BioXXX project"

Good point and it's something we'll have to stress during the  
introduction of our talk.

> - I/O for different sequence format : this is the original primary  
> goal of BioCocoa and indeed the most important, because nobody  
> wants to have to deal with that. Imagine if you had to read jpg  
> files the old way  and implement your own decompression algorithm  
> when using Cocoa!

The I/O is another thing that might make a good demo.

> Finally, who is going to prepare the slides ;-)
> It looks like Peter/Alex/Tom are good candidates for that....

I'm definitely willing to help and to present (the introduction) part  
of the talk. I think Alex, Phil and Charles (I hope you'll be there  
Charles) are better placed to discuss implementation details. And of  
course, I hope to give the BLAST demo ;-))

Alex, how are we going to divide the work? Do you have a Keynote  
template we can use to create slides?



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