<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Guys,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>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:</DIV><DIV><DIV><DIV><BR class="khtml-block-placeholder"></DIV><BLOCKQUOTE type="cite"><DIV style=""> I want to give some suggestions for the presentation.<BR style=""><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Topics being covered during presentation:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- introduction to BioCocoa</DIV></BLOCKQUOTE><DIV style="">Phil: Motivation, why we are doing this. Especially why cocoa and not using biojava or other frameworks.</DIV></DIV></BLOCKQUOTE>Good point!</DIV><BLOCKQUOTE type="cite">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"</BLOCKQUOTE>Yep.</DIV><DIV><BLOCKQUOTE type="cite">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.</BLOCKQUOTE>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...<BR><DIV><BR><BLOCKQUOTE type="cite"><DIV style=""><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- framework structure and layout</DIV></BLOCKQUOTE></DIV></BLOCKQUOTE><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">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.</DIV></BLOCKQUOTE><DIV>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.</DIV><BLOCKQUOTE type="cite"><DIV style=""><DIV style="">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.</DIV></DIV></BLOCKQUOTE><DIV>Yep, see above.</DIV><DIV><BLOCKQUOTE type="cite">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.</BLOCKQUOTE>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.<BR></DIV></DIV><DIV><BR><BLOCKQUOTE type="cite"><DIV style=""><BLOCKQUOTE type="cite"></BLOCKQUOTE><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- future plans</DIV></BLOCKQUOTE><DIV style="">Phil: This is the point we have to discuss in the list. what exactly everybody wants the framework to be. </DIV></DIV></BLOCKQUOTE><BLOCKQUOTE type="cite"><DIV style=""><DIV style=""> So i will start:</DIV><DIV style=""> Basic datastructures shoud be provided:</DIV><DIV style=""> Sequences, Alignments, Annotations, Protein Structures and more</DIV><DIV style=""> Classes to access common databases like genbank, pdb etc.</DIV><DIV style=""> I want to provide HMMs for sequence analysis</DIV></DIV></BLOCKQUOTE><BR><BLOCKQUOTE type="cite">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.</BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Charles: </DIV></BLOCKQUOTE><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- 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!</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- 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?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- the annotations: big thing... choosing a standard like the one proposed by Alex? maybe we could get some feedback and ideas from the audience.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- 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</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- 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?</DIV></BLOCKQUOTE></DIV><BR><BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">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.</DIV></BLOCKQUOTE>I agree, and another thing discuss how to do this during the WWDC. <BR><BR><DIV style=""><DIV style="">True, great suggestions!</DIV></DIV><BR><BLOCKQUOTE type="cite"><DIV style=""><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- Q&A, discussion</DIV></BLOCKQUOTE></DIV></BLOCKQUOTE><DIV><BLOCKQUOTE type="cite"></BLOCKQUOTE></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">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.</DIV></BLOCKQUOTE>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 necessary.<BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Peter: Are we also supposed to demo BC? ;-)</DIV></BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">That would be great, so yes, the BLAST demo would be nice! Furthermore, we have the peptides demo and the seqIO demo...</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">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.</DIV></BLOCKQUOTE>Good plan!<BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#001FD7">John: </FONT><FONT class="Apple-style-span" color="#001FD7">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.</FONT>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.<BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#001FD7">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.</FONT></DIV></DIV></BLOCKQUOTE><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; color: rgb(0, 0, 221); "><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; color: rgb(0, 0, 221); "><FONT class="Apple-style-span" color="#001FD7"><SPAN class="Apple-style-span" style="background-color: transparent;">Enjoy the trip, and send me a full report of WWDC. Hope they give you a neat gift at the keynote -</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ; color: rgb(0, 0, 221); "><FONT class="Apple-style-span" color="#001FD7"></FONT></DIV></DIV></BLOCKQUOTE>Great work on the descriptions!!! That will be certainly helpful!! We'll keep you all informed on the things happening at WWDC!</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Koen: Shall I announce it also on Apple's scitech mailing list?</DIV></BLOCKQUOTE>Yes, please do!<BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Could you or Alex confirm what will be the right time and place?</DIV></BLOCKQUOTE></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">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.<BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><DIV>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!</DIV><DIV>Cheers,</DIV><DIV>Alex</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BLOCKQUOTE type="cite"><DIV style=""><BR style=""></DIV></BLOCKQUOTE></DIV></DIV></BODY></HTML>