[Biococoa-dev] WWDC 2005 BioCocoa meeting

Charles PARNOT charles.parnot at stanford.edu
Mon May 30 14:29:15 EDT 2005

Yes, long time, no mail!

I have been very busy with many different things (the big thing being the Tiger transition to Xgrid 1.0...) and BioCocoa has been in the backburner for a while. With the WWDC meeting, it is going to be in the frontburner again, at least for a few days... This is going to be a great opportunity to maybe get more feedback.

The topics planned for the meeting look good. There are several points that I want to make/add.

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.

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.

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"
- 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?

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


At 9:52 PM +0200 5/28/05, <a.griekspoor at nki.nl> wrote:
>Hi guys,
>It's a been quite a while and the BioCocoa mailinglist has come to a rest lately, but let's keep it on the silence before the storm. I spoke to a few a you already offlist already, but I would like to let you know that something is cooking underneath the surface. Due to personal circumstances it was unclear whether Tom and I would go to the WWDC at all, and this was one of the reasons I failed to pursue a BioCocoa meeting at the WWDC. Now the good news is that in the end there will be a BioCocoa meeting after all. Also, Tom and I will leave for SF this thursday. Also Phil and Peter will be there. Last week the scitech people of Apple contacted us if we would like a BioCocoa meeting to be organized. We have held a teleconference to discuss the different options and agreed on the  following:
>- Wednesday night from 19 (hands-on-lab) we will have reserved room to our availability.
>- We will give a short presentation followed by Q&A and dicussions.
>- A number of Apple staff people will be present in the audience.
>- The meeting will be announced during the WWDC and on the website (http://developer.apple.com/wwdc/sciencedev.html)
>Unfortunately, they could not sponsor any seats for non-scholarship candidates, although they might be able to arrange entrance at wednesday night for Charles who's located close by at Stanford. Together we will represent the BioCocoa team and will give a short presentation followed by a discussion session. Hopefully this leads to more interest in the project both from "users" and new developers. Perhaps it's nice to discuss the presentation details, discussion points on the list. The people at Apple asked me to write a short abstract and the topics of the meeting, which had to be done in under and hour, so please bare this in mind...
>More to follow....
>Here's the abstract for the BioCocoa meeting:
>BioCocoa is an opensource Cocoa framework for bioinformatics written in Objective-C. We intend to provide Cocoa programmers with a full suite of tools, to edit and manipulate biological sequence information. Initially started as framework to read and write the plethora of available sequence file formats, we work to make BioCocoa a more general bioframework leveraging the power of the objective-C language and Cocoa frameworks. Eventually, we aspire to become siblings of OpenBio.org projects like BioJava, BioPerl, BioRuby. During a short presentation and discussion session we would like to present the BioCocoa framework and discuss its possibilities. We welcome everybody interested in developing bioscience applications to join in and help us build the ideal foundation for the next generation Mac bio apps. See you there!
>URL: http://bioinformatics.org/project/?group_id=318
>Topics being covered during presentation:
>- introduction to BioCocoa
>- framework structure and layout
>- design principles and choices
>- current status
>- future plans
>- Q&A, discussion
>                    ** 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
>                  AIM: mekentosj at mac.com
>                 E-mail: a.griekspoor at nki.nl
>              Web: http://www.mekentosj.com
>              4Peaks - For Peaks, Four Peaks.
>       2004 Winner of the Apple Design Awards
>               Best Mac OS X Student Product
>             http://www.mekentosj.com/4peaks
>Biococoa-dev mailing list
>Biococoa-dev at bioinformatics.org

Help science go fast forward:

Charles Parnot
charles.parnot at stanford.edu

Room  B157 in Beckman Center
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Stanford, CA 94305 (USA)

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