From kvddrift at earthlink.net Tue May 10 22:13:39 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 10 May 2005 22:13:39 -0400 Subject: [Biococoa-dev] BCProteinStructure Message-ID: Hi, Just noticed a set of new classes have been added by Philipp to represent protein structures. Nice work! I assume these are to facilitate the reading of PDB files? Although I can see a wider use as well. What I really like is that the introduction of a BCAtom class will allow the definition of modifications and features on the atom-level (think oxidation, deamidation, di-sulfide bridges, DNA-damage). So it might be useful to incorporate the BCAtom class in BCSymbol. A few small comments (also see the 'new files' entry in the BioCocoa dev docs): All headers should be public in the Target (I already fixed this in cvs) BCFoundation should only import the Foundation headers, not all Cocoa headers (also fixed) @class declarations are enough in headers, unless you subclass another class, then you need to use #import (also fixed) One last question, since BCResidue is basically an amino acid, why not subclass BCAminoAcid? Or even, make BCResidue a subclass of BCSymbol, and make BCAminoAcid and BCNucleotide subclasses of BCResidue. Also, BCChain seems to be a replication of BCSequence so I am not sure yet what its added value can be. Other then that, I think it is an excellent addition to BioCocoa. cheers, - Koen. From biococoa at bioworxx.com Wed May 11 06:34:07 2005 From: biococoa at bioworxx.com (Philipp Seibel) Date: Wed, 11 May 2005 12:34:07 +0200 Subject: [Biococoa-dev] Re: BCProteinStructure In-Reply-To: References: Message-ID: <0692FF1E-5D55-4399-AB9B-1B0B59D4FA81@bioworxx.com> Hi, sorry not mentioning the addition yet, but my diploma thesis is coming to an end and i'm very busy. Perhaps you noticed the time i checked the new classes in ;-), i needed some time to relax in the evening, so i did something productive ..... programming new biococa structures ;-) ..... Am 11.05.2005 um 04:13 schrieb Koen van der Drift: > Hi, > > Just noticed a set of new classes have been added by Philipp to > represent protein structures. Nice work! I assume these are to > facilitate the reading of PDB files? thats what i want them for. > Although I can see a wider use as well. What I really like is that > the introduction of a BCAtom class will allow the definition of > modifications and features on the atom-level (think oxidation, > deamidation, di-sulfide bridges, DNA-damage). So it might be useful > to incorporate the BCAtom class in BCSymbol. > i completly agree. we just have to specify how to make annotations in general. really important for nearly every structural class (Sequences, Structures,etc.) > A few small comments (also see the 'new files' entry in the > BioCocoa dev docs): > All headers should be public in the Target (I already fixed this in > cvs) > BCFoundation should only import the Foundation headers, not all > Cocoa headers (also fixed) > @class declarations are enough in headers, unless you subclass > another class, then you need to use #import (also fixed) > > One last question, since BCResidue is basically an amino acid, why > not subclass BCAminoAcid? Or even, make BCResidue a subclass of > BCSymbol, and make BCAminoAcid and BCNucleotide subclasses of > BCResidue. Also, BCChain seems to be a replication of BCSequence so > I am not sure yet what its added value can be. > > Other then that, I think it is an excellent addition to BioCocoa. > > cheers, > > - Koen. > > cheers, Phil From a.griekspoor at nki.nl Sat May 28 15:52:48 2005 From: a.griekspoor at nki.nl (a.griekspoor at nki.nl) Date: Sat, 28 May 2005 21:52:48 +0200 Subject: [Biococoa-dev] WWDC 2005 BioCocoa meeting Message-ID: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> 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.... Cheers, Alex 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 ********************************************************* From kvddrift at earthlink.net Sat May 28 16:31:46 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 28 May 2005 16:31:46 -0400 Subject: [Biococoa-dev] WWDC 2005 BioCocoa meeting In-Reply-To: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> References: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> Message-ID: <18e91c9ac9913d957d0eff831c45a2d8@earthlink.net> Hi Alex, This is absolutely fantastic! It is encouraging that Apple contacted you to organize the meeting. Thanks for setting this up. The abstract also looks fine to me. Too bad I cannot attend the meeting :( 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. - Koen. On May 28, 2005, at 3:52 PM, 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.... > Cheers, > Alex > > 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 > https://bioinformatics.org/mailman/listinfo/biococoa-dev > From biococoa at bioworxx.com Sat May 28 16:39:55 2005 From: biococoa at bioworxx.com (Philipp Seibel) Date: Sat, 28 May 2005 22:39:55 +0200 Subject: [Biococoa-dev] WWDC 2005 BioCocoa meeting In-Reply-To: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> References: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> Message-ID: <318EDC04-4A45-4341-BE14-730AC5039571@bioworxx.com> Hi all, great to hear about the meeting. I want to give some suggestions for the presentation. > Topics being covered during presentation: > > - introduction to BioCocoa Motivation, why we are doing this. Especially why cocoa and not using biojava or other frameworks. > - framework structure and layout 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. > - design principles and choices > - current status > - future plans 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 > - Q&A, discussion > so this were my fist sponaneous ideas. Phil -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sat May 28 17:02:52 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 28 May 2005 17:02:52 -0400 Subject: [Biococoa-dev] WWDC 2005 BioCocoa meeting In-Reply-To: <318EDC04-4A45-4341-BE14-730AC5039571@bioworxx.com> References: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> <318EDC04-4A45-4341-BE14-730AC5039571@bioworxx.com> Message-ID: <3be3c062130ba56236cc7ad3af7e6608@earthlink.net> On May 28, 2005, at 4:39 PM, Philipp Seibel wrote: > > 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. > > Good input Phillip. 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. - Koen. From peter.schols at bio.kuleuven.be Sun May 29 06:36:52 2005 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Sun, 29 May 2005 12:36:52 +0200 Subject: [Biococoa-dev] WWDC 2005 BioCocoa meeting In-Reply-To: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> References: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> Message-ID: <076F8E02-5DDA-43F3-9960-8EED799670FE@bio.kuleuven.be> Hi Alex, It sounds like the teleconference was worth it... ;-) Please let us know how we will/can divide the work. I'm willing to help with the organisation of the presentation and discussion. Are we also supposed to demo BC? ;-) Best wishes, Peter On 28 May 2005, at 21:52, 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.... > Cheers, > Alex > > 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 > https://bioinformatics.org/mailman/listinfo/biococoa-dev > > From james.balhoff at duke.edu Sun May 29 10:46:49 2005 From: james.balhoff at duke.edu (Jim Balhoff) Date: Sun, 29 May 2005 10:46:49 -0400 Subject: [Biococoa-dev] WWDC 2005 BioCocoa meeting In-Reply-To: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> References: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> Message-ID: <127FA211-DE48-4D84-A9AD-05F42E915EB0@duke.edu> Hey guys, I've pretty much been silent for several months now, but I will be at WWDC and will definitely be at any BioCocoa events. Just wanted to let you know so you can keep me posted. Thanks, Jim ____________________________________________ James P. Balhoff National Evolutionary Synthesis Center Dept. of Biology Duke University Durham, NC 27708-0338 USA From biococoa at bioworxx.com Sun May 29 12:01:52 2005 From: biococoa at bioworxx.com (Philipp Seibel) Date: Sun, 29 May 2005 18:01:52 +0200 Subject: [Biococoa-dev] WWDC 2005 BioCocoa meeting In-Reply-To: <127FA211-DE48-4D84-A9AD-05F42E915EB0@duke.edu> References: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> <127FA211-DE48-4D84-A9AD-05F42E915EB0@duke.edu> Message-ID: Hey Jim, nice to hear. May i ask, whether you want to use or participate in developing the framework. To keep one point clear, no matter what your answer is, we will keep you informed about any such event. ;-) cheers, Phil > Hey guys, > > I've pretty much been silent for several months now, but I will be > at WWDC and will definitely be at any BioCocoa events. Just wanted > to let you know so you can keep me posted. > > Thanks, > Jim From kvddrift at earthlink.net Sun May 29 15:27:31 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 29 May 2005 15:27:31 -0400 Subject: [Biococoa-dev] Annotation questions Message-ID: Hi, Spent some time today on BCSequenceReader to include more annotations. For the SwissProt format (and probably other formats as well), some annotations are in multiple lines. So I modified the - (void) addAnnotation:(NSString *)annotation forKey: (NSString *) key to test for existing keys. In that case I am appending the annotation, instead of replacing it. Right now, the code in readSwissProt now first creates an dummy sequence, then iterates over all the lines to add th e annotations, and then needs to add the sequence to the BCSequence object. Currently there is no 'setSequence' method, so I choose to create another BCSequence object with the sequencestring, and then copy the annotations from the dummy object to the real object. However, the setAnnotations method was commented out. Are there any objections if I uncomment that? Another approach could be to move the addAnnotation from BCAbstractSequence to BCSequenceReader. Also, we need to think how to implement nested annotations. The easiest would be to make a BCAnnotations object as the value for another BCAnnotation. Let me know what you think, cheers, - Koen. From biococoa at bioworxx.com Sun May 29 16:04:56 2005 From: biococoa at bioworxx.com (Philipp Seibel) Date: Sun, 29 May 2005 22:04:56 +0200 Subject: [Biococoa-dev] Annotation questions In-Reply-To: References: Message-ID: <6C8EF642-149F-423F-BE15-46BB397AFBA9@bioworxx.com> Hey Koen, nice to hear something going on. > Hi, > > Spent some time today on BCSequenceReader to include more > annotations. For the SwissProt format (and probably other formats > as well), some annotations are in multiple lines. So I modified the > - (void) addAnnotation:(NSString *)annotation forKey: (NSString *) > key to test for existing keys. In that case I am appending the > annotation, instead of replacing it. > > Right now, the code in readSwissProt now first creates an dummy > sequence, then iterates over all the lines to add th e annotations, > and then needs to add the sequence to the BCSequence object. > Currently there is no 'setSequence' method, so I choose to create > another BCSequence object with the sequencestring, and then copy > the annotations from the dummy object to the real object. However, > the setAnnotations method was commented out. Are there any > objections if I uncomment that? > > Another approach could be to move the addAnnotation from > BCAbstractSequence to BCSequenceReader. > > Also, we need to think how to implement nested annotations. The > easiest would be to make a BCAnnotations object as the value for > another BCAnnotation. The Annotation and Feature stuff has to be designed very carefully. Btw i need it as well in my ProteinStructure classes. I think using dictionaries and dictionaries in dictionaries are a solution, but very difficult to understand for the user of the framework. On the other hand it's very flexible and could be easily saved as a .plist. So we should consider where we will need it in the future. I think features are even more difficult to realize, because they could have the same key and have a special order. Finaly i would suggest to discuss at least for 2 - 3 weeks, what we want to do with features and annotations and of course where they appear in "real life". We should take the time, because this is a very fundamental structure. I would also suggest to look at the implementations of BioJava and the others. Btw. is there a BioJava user in our group, to tell about pros and cons of their implementation. Ok so far from me ..... cheers, Phil From kvddrift at earthlink.net Sun May 29 16:13:44 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 29 May 2005 16:13:44 -0400 Subject: [Biococoa-dev] Annotation questions In-Reply-To: <6C8EF642-149F-423F-BE15-46BB397AFBA9@bioworxx.com> References: <6C8EF642-149F-423F-BE15-46BB397AFBA9@bioworxx.com> Message-ID: <3eceb67f4a572ed37fd8ebd36fc66d52@earthlink.net> On May 29, 2005, at 4:04 PM, Philipp Seibel wrote: > The Annotation and Feature stuff has to be designed very carefully. > Btw i need it as well in my ProteinStructure classes. I think using > dictionaries and dictionaries in dictionaries are a solution, but very > difficult to understand for the user of the framework. On the other > hand it's very flexible and could be easily saved as a .plist. So we > should consider where we will need it in the future. I think features > are even more difficult to realize, because they could have the same > key and have a special order. > > Finaly i would suggest to discuss at least for 2 - 3 weeks, what we > want to do with features and annotations and of course where they > appear in "real life". We should take the time, because this is a very > fundamental structure. I would also suggest to look at the > implementations of BioJava and the others. Btw. is there a BioJava > user in our group, to tell about pros and cons of their > implementation. Ok so far from me ..... This sounds like an excellent subject to discuss at WWDC :) - Koen. From kvddrift at earthlink.net Sun May 29 18:08:54 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 29 May 2005 18:08:54 -0400 Subject: [Biococoa-dev] Annotation questions In-Reply-To: References: Message-ID: <0bc6547784c6fd555d453d80f3274f58@earthlink.net> I just commited the code in cvs, so everyone can have a look what I am talking about :) If the approach in readSwissProtFile seems good, I will update other read... methods as well. cheers, - Koen. On May 29, 2005, at 3:27 PM, Koen van der Drift wrote: > Hi, > > Spent some time today on BCSequenceReader to include more annotations. > For the SwissProt format (and probably other formats as well), some > annotations are in multiple lines. So I modified the - (void) > addAnnotation:(NSString *)annotation forKey: (NSString *) key to test > for existing keys. In that case I am appending the annotation, instead > of replacing it. > > Right now, the code in readSwissProt now first creates an dummy > sequence, then iterates over all the lines to add th e annotations, > and then needs to add the sequence to the BCSequence object. > Currently there is no 'setSequence' method, so I choose to create > another BCSequence object with the sequencestring, and then copy the > annotations from the dummy object to the real object. However, the > setAnnotations method was commented out. Are there any objections if I > uncomment that? > > Another approach could be to move the addAnnotation from > BCAbstractSequence to BCSequenceReader. > > Also, we need to think how to implement nested annotations. The > easiest would be to make a BCAnnotations object as the value for > another BCAnnotation. > > Let me know what you think, > > cheers, > > - Koen. > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > From james.balhoff at duke.edu Sun May 29 19:01:57 2005 From: james.balhoff at duke.edu (Jim Balhoff) Date: Sun, 29 May 2005 19:01:57 -0400 Subject: [Biococoa-dev] WWDC 2005 BioCocoa meeting In-Reply-To: References: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> <127FA211-DE48-4D84-A9AD-05F42E915EB0@duke.edu> Message-ID: I suppose at the moment I would call myself a user, although I did contribute one line of code long, long ago. Hopefully I will be able to contribute in some way in the future. I had to take a long break from Cocoa in order to get my research and dissertation done. :-) Jim On May 29, 2005, at 12:01 PM, Philipp Seibel wrote: > Hey Jim, > > nice to hear. May i ask, whether you want to use or participate in > developing the framework. > > To keep one point clear, no matter what your answer is, we will > keep you informed about any such event. ;-) > > cheers, > Phil From kvddrift at earthlink.net Mon May 30 14:01:11 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 30 May 2005 14:01:11 -0400 Subject: [Biococoa-dev] Annotation questions In-Reply-To: <7586B9F4-3203-47E4-AA34-21FF9DD0913C@bio.kuleuven.be> References: <0bc6547784c6fd555d453d80f3274f58@earthlink.net> <7586B9F4-3203-47E4-AA34-21FF9DD0913C@bio.kuleuven.be> Message-ID: On May 30, 2005, at 3:58 AM, Peter Schols wrote: > So to conclude: I think one of the priorities at WWDC will be to make > a decision about a class that will hold multiple sequences. Once > that's done, we can rewrite all I/O methods at once and I'll add the > code for the additional formats. > Sounds like a good plan :) 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. - Koen. From charles.parnot at stanford.edu Mon May 30 14:29:15 2005 From: charles.parnot at stanford.edu (Charles PARNOT) Date: Mon, 30 May 2005 11:29:15 -0700 Subject: [Biococoa-dev] WWDC 2005 BioCocoa meeting In-Reply-To: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> References: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> Message-ID: 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 ?-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.... charles At 9:52 PM +0200 5/28/05, 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.... >Cheers, >Alex > >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 >https://bioinformatics.org/mailman/listinfo/biococoa-dev -- Help science go fast forward: http://cmgm.stanford.edu/~cparnot/xgrid-stanford/ Charles Parnot charles.parnot at stanford.edu Room B157 in Beckman Center 279, Campus Drive Stanford University Stanford, CA 94305 (USA) Tel +1 650 725 7754 Fax +1 650 725 8021 From kvddrift at earthlink.net Mon May 30 15:09:46 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 30 May 2005 15:09:46 -0400 Subject: [Biococoa-dev] WWDC 2005 BioCocoa meeting In-Reply-To: References: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> Message-ID: <1e1243bfdfbe069e318339e44ee211cd@earthlink.net> On May 30, 2005, at 2:29 PM, Charles PARNOT wrote: > - 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? > Good points, Charles. Hope you can make it into the meeting. Another important point I just thought of after reading Charles' mail. 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. - Koen. From kvddrift at earthlink.net Mon May 30 15:33:24 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 30 May 2005 15:33:24 -0400 Subject: Fwd: [Biococoa-dev] WWDC 2005 BioCocoa meeting Message-ID: <0ebc64383937233594a500425c9b595f@earthlink.net> forgot to include the mailing list :) Begin forwarded message: > From: Koen van der Drift > Date: May 30, 2005 3:15:52 PM EDT > To: > Subject: Re: [Biococoa-dev] WWDC 2005 BioCocoa meeting > > > On May 28, 2005, at 3:52 PM, wrote: > >> - The meeting will be announced during the WWDC and on the website >> (http://developer.apple.com/wwdc/sciencedev.html) >> > > Shall I announce it also on Apple's scitech mailing list? > > - Koen. > From peter.schols at bio.kuleuven.be Mon May 30 15:38:23 2005 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Mon, 30 May 2005 21:38:23 +0200 Subject: [Biococoa-dev] Annotation questions In-Reply-To: References: <0bc6547784c6fd555d453d80f3274f58@earthlink.net> <7586B9F4-3203-47E4-AA34-21FF9DD0913C@bio.kuleuven.be> Message-ID: I fully agree! While CoreData is great (I'm using it for a new app and the reduction in development time by using it is just amazing) I think we should stay compatible with 10.3 for a while... On 30 May 2005, at 20:01, Koen van der Drift wrote: > > On May 30, 2005, at 3:58 AM, Peter Schols wrote: > > >> So to conclude: I think one of the priorities at WWDC will be to >> make a decision about a class that will hold multiple sequences. >> Once that's done, we can rewrite all I/O methods at once and I'll >> add the code for the additional formats. >> >> > > Sounds like a good plan :) 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. > > - Koen. > > From kvddrift at earthlink.net Mon May 30 15:53:06 2005 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 30 May 2005 15:53:06 -0400 Subject: [Biococoa-dev] WWDC 2005 BioCocoa meeting In-Reply-To: References: <0ebc64383937233594a500425c9b595f@earthlink.net> Message-ID: <8299353d6f309d4aeebfa63a4eaabba7@earthlink.net> On May 30, 2005, at 3:39 PM, Peter Schols wrote: > Please do, great idea! > > Before I do that, I want to be sure that I got the time right, I don't see it (yet) announced on Apple's website: http://developer.apple.com/wwdc/labs_schedule/labs_wednesday_pm.html Could you or Alex confirm what will be the right time and place? thanks, - Koen. From peter.schols at bio.kuleuven.be Mon May 30 16:09:46 2005 From: peter.schols at bio.kuleuven.be (Peter Schols) Date: Mon, 30 May 2005 22:09:46 +0200 Subject: [Biococoa-dev] WWDC 2005 BioCocoa meeting In-Reply-To: References: <667464FDA2C81D4CA79D7F3B728D10E73C15F3@adsrv100.nki.nl> Message-ID: 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 ?-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? Thanks! Peter From jtimmer at bellatlantic.net Tue May 31 11:35:28 2005 From: jtimmer at bellatlantic.net (John Timmer) Date: Tue, 31 May 2005 11:35:28 -0400 Subject: [Biococoa-dev] WWDC 2005 BioCocoa meeting In-Reply-To: Message-ID: Hi, all - 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 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 - John Design of BCFoundation Biological information is generally conveyed as an ordered sequence of fundamental units, typically nucleotide bases or amino acids. Interpretation and transformation of these units is typically carried out by enzymes or collections of enzymes (ie - ribosomes). We have attempted to make BioCocoa's Foundation reflect this organization. The fundamental information carrying units belong to the BCSymbol class, which has subclasses for all the individual types of unit. Specific collections of related symbols (ie - all amino acids) are available through the BCSymbolSet class. Ordered arrays of these units are managed through BCSequence and its subclasses. The transformation or extraction of information from these sequences is managed by subclasses of BCTools. The function and design philosophy of each class is discussed in detail below. Several additional functions are provided by other groups of classes, such as BCAlignment and BCGenetic code; these are discussed following the description of these core classes. Intelligent Objects: BCSymbols In many biological frameworks, amino acids and nucleotides are stored as char's. Although very lightweight, char's cannot provide any information regarding the biological object they are representing; information must be obtained by looking it up based on the char value. This limits the application of object-oriented design, and adds to code complexity, as each information lookup will occur in different sections of code, and may be accomplished by different means in each place. We have taken an opposite approach: each nucleotide and amino acid is a full-featured object which conveys relevant information about its properties, ranging from the complement(s) of a nucleotide to the pKA of an amino acid. To allow the rapid addition of new information to these Symbols, the properties are stored in an Apple-standard property list file. Each symbol retains its entire entry in this file throughout its lifetime, and its properties are accessible via a "valueForKey:" message using the appropriate key. Thus, adding a new property (for example, the frequency at which it occurs in an alpha-helix) to all amino acids is as simple as editing an XML file. Retrieving that value can then be done with [aSymbol valueForKey: @"alpha helicity"];. For code efficiency reasons, many of the basic properties are also stored as ivars and accessible by standard methods. This allows each symbol to be a repository for relevant information, with a standardized method of looking up that information. It also greatly simplifies the writing of methods that retrieve information from all symbols in a sequence. For example, a molecular weight calculation can be as simple as the following: for ( i = 0; i < [theSequence length]; i++ ) molecularWeight = molecularWeight + [[theSequence symbolAtIndex: i] molecularWeight]; To keep memory use to a minimum, each symbol is maintained as a singleton. In other words, every sequence that has an alanine has a pointer to the single alanine instance in its place. Symbols are typically accessed one of two ways: Either via a call to the appropriate class method using the unichar symbol, or via a named class method, such as [BCAminoAcid alanine]. This allows the relationships between symbols (ie - complement) to be stored in the property list file - Symbol pointers can be generated by using the string "alanine" as a selector. Alternately, a string formatted sequence can be translated into a symbol array simply by passing each of its characters to the appropriate class method. Each symbol type also has gap and undefined symbols. The symbols are also grouped within Symbol Sets. Several such sets are pre-made singletons - for example, all non-ambiguous ribose nucleotides, all non-gap and undefined amino acids, etc. Symbol sets are primarily used to provide internal consistency when symbols are combined into a sequence. As You Like it: the BCSequence class cluster The BCSequence class cluster is an effort to balance a set of competing issues. In many cases (file format conversions, mass calculations), the specific type of sequence is irrelevant to the developer, and a generic sequence class provides all the functionality needed. In other cases (complementation, translation), providing the appropriate sequence type - a nucleotide sequence - will provide developers finer control and prevent errors. To provide for both needs, BCSequences are implemented as a class cluster. Any sequence can be created and used as either a generic sequence class, or a specific subclass - headers for each are included in the framework. Control of the sequence type and its composition can also be done at the level of setting its Symbol Set. A sequence's Symbol Set both defines the sequence type (ie - DNA, amino acid) and potentially limits its composition (ie - all non-ambiguous RNA bases). This design creates one issue, however: how should methods that only act on a specific sequence type be organized and structured when they may be handed a generic sequence type? We are grouping the methods that act on one or more sequence types in the BCTools section. A tool is always initialized using a generic sequence. If it's initialized with a sequence it can't operate on (say, the BCComplementTool initialized with a protein sequence), it always returns a copy of the sequence when any transformation is requested of it. If it can operate on the sequence, everything works normally. Wherever possible, convenience methods have been added to the appropriate subclasses that will initialize any tools that can act on that sequence type in a way that's guaranteed to work. -------------- next part -------------- An HTML attachment was scrubbed... URL: