[Biococoa-dev] WWDC 2005 BioCocoa meeting

Alexander Griekspoor a.griekspoor at nki.nl
Wed Jun 1 04:34:24 EDT 2005

Hi Guys,

Sorry for replying so late, packed my bags and from thursday BC will  
be a main focus finally again ;-) Great input on the presentation, I  
will try to summarize all emails below. Let's continue the  
discussions and I propose to those in SF next week to meet and  
prepare all stuff on monday and tuesday. So here we go:

>  I want to give some suggestions for the presentation.
>> Topics being covered during presentation:
>> - introduction to BioCocoa
> Phil: Motivation, why we are doing this. Especially why cocoa and  
> not using biojava or other frameworks.
Good point!
> Charles: 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"
> Koen: We need to think of some good arguments why users want to use  
> BioCocoa instead of eg BioPerl or BioJava. Both are already very  
> advanced, and work on OS X, so why would a user want to jump into a  
> very early BioCocoa? Of course, it is a Cocoa/ObjC framework, so  
> it's very easily to implement into native programs. However, as we  
> already have discussed, because we stuff everything in NSObject  
> subclasses, we add quite some overhead. Maybe this is also an issue  
> to discuss at WWDC.
I think it's clear what we have to discuss in the intro ;-) I've said  
it before often during our discussions, I wish I could talk to people  
from Apple/Next about the way they dealt with object overhead, and  
would like to know what goes on under the hood when you use NSString  
or NSAttributedString for example. It would be nice to find that out  
at the WWDC...

>> - framework structure and layout
> Koen: I think one thing that could be discussed is our current  
> framework design. We've already gone through a couple of iterations  
> and I think we rather not want to go through that again ;).  
> However, it will be at the base of the rest of the code, and I  
> think it would be good to get some input on it. Now is the time to  
> make adjustments before we start adding a lot more code to it.
Absolutely, this is a great opportunity to discuss the design choices  
we made. According to Robert Kehrer a few Apple staff people would be  
present, and it would be a great to ask their opinion on these  
matters, especially people from the cocoa frameworks. Perhaps we can  
all try to speak about these issues when we meet the cocoa engineers  
in for instance the hands-on-labs.
> Phil: This is what i especially want to talk about. I have many  
> many things to contribute to the framework and we definitly need to  
> discuss where to place it.
Yep, see above.
> Charles: An other important idea related to that: a framework like  
> this had two sides: the inside and the outside(!). The inside = the  
> implementation details, the behind-the-scenes under-the-hood stuff.  
> The outside = the public interface. The WWDC might be a great  
> occasion to define the public interface more precisely and decide  
> what the potential users need. Maybe the details of the  
> implementation are not very important to discuss too much. WE  
> developers could discuss that between us, but this is not the thing  
> we will get  useful feedback in just a couple of hours from an  
> external audience. I am not saying we should not talk at all about  
> it, but that we should just discuss it in general.
Very true, perhaps it's nice to see it it in the following way, the  
BioCocoa meeting might be ideal to focus indeed on the outside. At  
the same time, it would again be great if everyone of us could  
discuss the inside with experienced people like Apple engineers. This  
info can then be fed back in our discussions.

>> - future plans
> Phil: This is the point we have to discuss in the list. what  
> exactly everybody wants the framework to be.
>     So i will start:
>     Basic datastructures shoud be provided:
>     Sequences, Alignments, Annotations, Protein Structures and more
>     Classes to access common databases like genbank, pdb etc.
>     I want to provide HMMs for sequence analysis

> Koen: For me the things that need to be added are I/O of various  
> sequences, with the addition of reading them from a database, maybe  
> by using webkit? Also features and annotations are important, at  
> least for me.

> Charles:
> - 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 BCSequence et al classes : right now, they are not very  
> powerful (on the outside!), and the interface is very simple; but  
> the core of it is there and quite nice now (and with tests!!);  
> there are still two questions about the design: do we need mutable/ 
> immutable classes? do we need to go to CoreData?
> - the annotations: big thing... choosing a standard like the one  
> proposed by Alex? maybe we could get some feedback and ideas from  
> the audience.
> - some prebuilt NSViews for GUI app... at this point, they should  
> not be too elaborate, but could be useful to have something to work  
> with and test things and get a better sense of what BioCocoa can  
> become
> - the tools: BioPerl is a lot about wrapping the plethora of  
> existing CLI tools for biology; is this what we want to do too? it  
> does not look like it, but this is worth discussing maybe; it seems  
> from the mailing list and what people are doing is that we want to  
> integrate some of the most common algorithms in the code  
> (alignments, digests, sequence searches,...). However, do we still  
> want to provide an interface to other more specialized tools, or is  
> it not the point of BioCocoa? or something in the far future?

> Koen: Also I would like to suggest that we don't yet implement  
> CoreData, since many people (including me) are still running 10.3.  
> Or at least make it an extension.
I agree, and another thing discuss how to do this during the WWDC.

True, great suggestions!

>> - Q&A, discussion

> Peter: Please let us know how we will/can divide the work. I'm  
> willing to help with the organisation of the presentation and  
> discussion.
Let's prepare the definitive presentation at the WWDC together,  
including the division of who will tell what. I can try to make a  
template beforehand, but usually that's changed very easy later of  

> Peter: Are we also supposed to demo BC? ;-)
That would be great, so yes, the BLAST demo would be nice!  
Furthermore, we have the peptides demo and the seqIO demo...
> Charles: 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.
Good plan!

John: Great news on the presentation – I’m just disappointed I won’t  
be able to go to California to meet with the rest of you.  If any of  
you have stopovers in NYC on the way to California, though, get in  
touch.I'm sorry that I have not been able to pursue more a possible  
sponsorship, it's a pity you can't be there John. Well, next time we  
make it work.
> I spent the weekend too loaded up on flu medication to actually do  
> any coding, but I threw together a quick start of a description of  
> the Foundation classes.  If any of you find it useful for getting  
> the presentation started, please use anything you like.  If you  
> find it incoherent, I blame the medicine.
> Enjoy the trip, and send me a full report of WWDC.  Hope they give  
> you a neat gift at the keynote -
Great work on the descriptions!!! That will be certainly helpful!!  
We'll keep you all informed on the things happening at WWDC!

> Koen: Shall I announce it also on Apple's scitech mailing list?
Yes, please do!
> Could you or Alex confirm what will be the right time and place?
It's at 7pm, in the room of the WWDC Science Connection. It should  
appear on the website, but I haven't seen it yet.

Ok, let me know what you think and what is there to be added to the  
things brought up. I propose to send all emails about where, when and  
what with regard to the meeting to the list so everyone present will  
know the plans. Perhaps it's nice to email all of you our cell phone  
numbers so we can get in contact if necessary (off list of  
course ;-). I can gather them first and send them to all wwdc  
participants... CU soon guys!

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