From kvddrift at earthlink.net Tue Aug 8 22:04:45 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 8 Aug 2006 22:04:45 -0400 Subject: [Biococoa-dev] BioCocoa 2.0 release Message-ID: <9422A519-C5DD-4842-903A-4762C2580651@earthlink.net> The BioCocoa team is pleased to announce the release of version 2.0 of the BioCocoa framework. BioCocoa is an open source Cocoa framework for bioinformatics written in Objective-C. We intend to provide Cocoa programmers with a full suite of tools for handling and manipulating biological sequences. This new release is a complete rewrite of the original BioCocoa framework which was written by Peter Schols. The new release includes: ? A set of model objects to represent biological sequences that are both easy to use, yet very powerful and lightweight. ? I/O classes to import and export sequences to and from a variety of commonly used formats, eg swiss-prot, ncbi, fasta. ? Tools to manipulate and obtain information about sequences. ? An NSTextView based class to display sequences. Initially started as framework to read and write the plethora of available sequence file formats, we continue to 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 such as BioJava, BioPerl, and BioRuby. For more information and to download the framework, please visit our website: http://bioinformatics.org/biococoa/ From sweetcocoa at mac.com Thu Aug 10 01:55:52 2006 From: sweetcocoa at mac.com (Peter Schols) Date: Wed, 9 Aug 2006 22:55:52 -0700 Subject: [Biococoa-dev] BioCocoa 2.0 release In-Reply-To: <9422A519-C5DD-4842-903A-4762C2580651@earthlink.net> References: <9422A519-C5DD-4842-903A-4762C2580651@earthlink.net> Message-ID: <2E399676-0318-4EBC-BA61-B3D8C22A7EAE@mac.com> Hi Koen, This seems to be the original press release, not the updated one (see below) cheers, peter BioCocoa 2: an open-source Cocoa framework for molecular biology SAN FRANCISCO -- August 9, 2006 -- The BioCocoa team is pleased to announce the release of BioCocoa 2.0 BioCocoa is an open-source framework for bioinformatics written in Objective-C. It intends to provide Cocoa programmers with a full suite of tools for handling and manipulating biological sequences. The new release includes: * A set of easy-to-use, yet powerful model objects representing biological sequences * I/O classes to import and export sequences to and from a variety of commonly used formats, eg swiss-prot, ncbi, fasta, nexus,... * Tools to manipulate and obtain information about sequences * An NSTextView subclass designed for sequence display Initially started as framework to read and write the plethora of available sequence file formats, BioCocoa is now evolving into a more general bioframework leveraging the power of the Objective-C language and Cocoa frameworks. More information and documentation about the framework is available at: http://bioinformatics.org/biococoa/ The framework can be downloaded directly at: http:// bioinformatics.org/biococoa/XXXXX.dmg The BioCocoa project has been founded by Peter Schols and has been expanded to include developers from around the world, including Koen van der Drift, Alexander Griekspoor, Charles Parnot and Philipp Seibel. The team welcomes new developers with a background in life sciences or bioinformatics and aims to make BioCocoa a sibling of other OpenBio.org projects such as BioJava, BioPerl, and BioRuby. On 08 Aug 2006, at 19:04, Koen van der Drift wrote: > The BioCocoa team is pleased to announce the release of version 2.0 > of the BioCocoa framework. > > BioCocoa is an open source Cocoa framework for bioinformatics > written in Objective-C. We intend to provide Cocoa programmers with > a full suite of tools for handling and manipulating biological > sequences. > > This new release is a complete rewrite of the original BioCocoa > framework which was written by Peter Schols. > > The new release includes: > > ? A set of model objects to represent biological sequences that are > both easy to use, yet very powerful and lightweight. > > ? I/O classes to import and export sequences to and from a variety > of commonly used formats, eg swiss-prot, ncbi, fasta. > > ? Tools to manipulate and obtain information about sequences. > > ? An NSTextView based class to display sequences. > > > Initially started as framework to read and write the plethora of > available sequence file formats, we continue to 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 such as BioJava, BioPerl, > and BioRuby. > > > For more information and to download the framework, please visit > our website: http://bioinformatics.org/biococoa/ > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From kvddrift at earthlink.net Thu Aug 10 04:01:42 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 10 Aug 2006 04:01:42 -0400 Subject: [Biococoa-dev] BioCocoa 2.0 release In-Reply-To: <2E399676-0318-4EBC-BA61-B3D8C22A7EAE@mac.com> References: <9422A519-C5DD-4842-903A-4762C2580651@earthlink.net> <2E399676-0318-4EBC-BA61-B3D8C22A7EAE@mac.com> Message-ID: <8F23929D-4601-4D4E-B9B9-197D10BA79B2@earthlink.net> Peter, Thanks for the correction, I have also added the correct url to download the project: > The framework can be downloaded directly at: http:// > bioinformatics.org/biococoa/XXXXX.dmg http://bioinformatics.org/biococoa/downloads/BioCocoa.dmg I am sure with the next release we will do it right in the first attempt ;-) And now for the big question, how's the WWDC going? cheers, - Koen. From sweetcocoa at mac.com Thu Aug 10 11:13:23 2006 From: sweetcocoa at mac.com (Peter Schols) Date: Thu, 10 Aug 2006 08:13:23 -0700 Subject: [Biococoa-dev] BioCocoa 2.0 release In-Reply-To: <8F23929D-4601-4D4E-B9B9-197D10BA79B2@earthlink.net> References: <9422A519-C5DD-4842-903A-4762C2580651@earthlink.net> <2E399676-0318-4EBC-BA61-B3D8C22A7EAE@mac.com> <8F23929D-4601-4D4E-B9B9-197D10BA79B2@earthlink.net> Message-ID: <8F9B9B70-AC9B-4A9D-89CE-E8B3F87AEE80@mac.com> Great, thanks! The poster generated quite some interest, yesterday. And some potential new contributors. Have to run now... peter On 10 Aug 2006, at 01:01, Koen van der Drift wrote: > Peter, > > Thanks for the correction, I have also added the correct url to > download the project: > >> The framework can be downloaded directly at: http:// >> bioinformatics.org/biococoa/XXXXX.dmg > > > http://bioinformatics.org/biococoa/downloads/BioCocoa.dmg > > > I am sure with the next release we will do it right in the first > attempt ;-) > > > And now for the big question, how's the WWDC going? > > > > cheers, > > - Koen. From davide.cittaro at ifom-ieo-campus.it Thu Aug 10 11:32:05 2006 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Thu, 10 Aug 2006 17:32:05 +0200 Subject: [Biococoa-dev] Reading blast formatted files Message-ID: <3E85B19B-58C6-4E3E-9AE1-58C81EB8731B@ifom-ieo-campus.it> Hi there, I'm new to BioCocoa (well, I've discovered it yesterday) and pretty new to Cocoa programming. I would like to start using this framework for some proteomics app. I would like to know if there is a way to read database formatted for NCBI blast with formatdb. Ok, I'm also going to read the documentation! d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303355 e-mail: davide.cittaro at ifom-ieo-campus.it */ -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Thu Aug 10 11:31:53 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 10 Aug 2006 11:31:53 -0400 (GMT-04:00) Subject: [Biococoa-dev] The future of BioCocoa Message-ID: <7455764.1155223913762.JavaMail.root@elwamui-polski.atl.sa.earthlink.net> Hi all, First of all I would like to officially congratulate Alex & Tom on behalf of the complete BioCocoa team with winning their second Apple Design Award, this time for EnzymeX in the Scientific category. Of course we can all be a bit extra proud, because EnzymeX uses the BioCocoa framework, albeit the older version. Now that we have finally released BioCocoa 2.0, based on the new framework structure, this is a good time to look ahead, and see what's in the future for the project. Although the project has been pretty quiet on this mailing list, a lot has been going on behind the scenes regarding the activities at this years WWDC. This could not be discussed on the mailinglist, because of the tight NDA's that Apple poses regarding such big events. I can let you know now that BioCocoa has a lot of exposure this year, including a poster, a podcast (!), and a demonstration. As soon as the WWDC is over, these will all be posted on our new and improved website. Another issue that was discussed off-line was that in order to keep the project going, one or two project leaders are necessary to set goals, timelines, and to keep people involved and motivated. I am pleased to announce that I have accepted that responsibility for at least one year. This doesn't mean that others have no more saying in the project and are only allowed to code ;-) As far as I am concerned we should still be discussing issues here on the mailinglist like we used to. I just hope that we don't just discuss stuff, but that we also actually improve and extend the framework by writing code. One of the conditions to accept the project leader position was that I didn't want yet another complete rewrite of the framework. So you can imagine I became a bit worried when I read the following on the WWDC diary from Alex: "... but with the four we went for dinner, ending up at the same place as last year. Very nice evening, with quite some interesting ideas and heated discussions about the best architecture for BioCooca. Something to definitely work out further." We had a similar thing happening last year, which resulted in an actual great improvement of the framework (ie using NSData instead of NSString to store sequences). So I hope that the guys who were present at the time can explain a bit in detail what this was about. So what are the plans for the (near) future? I think first we need to see how many people are still interested in contributing to the project. Hopefully the WWDC will attract some new developers. We will find out about that soon, I hope. What I don't want to happen is a situation similar to last year. We had some great momentum during and after the WWDC, but unfortunately this died out soon. I understand everyone has other obligations, and open source projects are just voluntary work. However, there are many open source projects out there that *do* work under similar circumstances. So hopefully this burst of activities will keep the project alive and kicking for a bit longer. Being the project leader, I will post at least once a month on the mailinglist to discuss the status of the project. To keep things going, I think we can set up some goals for the project, and work towards future releases. Some of the outstanding items are: * add mutable sequences * finish conversion of the old BCReader and BCWriter classes * maintain the website and wiki site * extend the framework with new tools and functionalities * add new BCAppKit classes *.... So that's it for now. I hope there will be a lot of input, and that we are all going to be involved in keeping the project alive. I think this is a great project, and it can benefit us all and everyone who wants to use it. cheers, - Koen. From james.balhoff at duke.edu Thu Aug 10 11:35:18 2006 From: james.balhoff at duke.edu (Jim Balhoff) Date: Thu, 10 Aug 2006 11:35:18 -0400 Subject: [Biococoa-dev] Apple Design Award Message-ID: <799B759E-6B0B-43CF-9EA2-955AA1871F28@duke.edu> Congrats to Alex and Tom for their award for EnzymeX!!! Certainly good publicity for BioCocoa as well. - Jim ____________________________________________ James P. Balhoff National Evolutionary Synthesis Center Duke University 2024 West Main St., Suite A200 Durham, NC 27705 USA From kvddrift at earthlink.net Thu Aug 10 12:34:32 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Thu, 10 Aug 2006 12:34:32 -0400 (GMT-04:00) Subject: [Biococoa-dev] Reading blast formatted files Message-ID: <29348260.1155227673048.JavaMail.root@elwamui-lapwing.atl.sa.earthlink.net> Hi Davide, Welcome to BioCocoa! It would be great if the framework will be used in a proteomics app. Regarding the blast input. Right now we don't the possibility to read the specific NCBI database formats. However, it would be a welcome addition. What I understand, formatdb is a standalone CLI app, correct? We need to look into if we can add this (because of possible license issues). Otherwise, we can write our own class, based on the formatdb source code. I encourage you to look into that possibility, we can help here to convert it to Objective-C and Cocoa. cheers, - Koen. -----Original Message----- >From: Davide Cittaro >Sent: Aug 10, 2006 11:32 AM >To: BioCocoa Mailinglist >Subject: [Biococoa-dev] Reading blast formatted files > >Hi there, I'm new to BioCocoa (well, I've discovered it yesterday) >and pretty new to Cocoa programming. I would like to start using this >framework for some proteomics app. >I would like to know if there is a way to read database formatted for >NCBI blast with formatdb. Ok, I'm also going to read the documentation! > >d >/* >Davide Cittaro >HPC and Bioinformatics Systems @ Informatics Core > >IFOM - Istituto FIRC di Oncologia Molecolare >via adamello, 16 >20139 Milano >Italy > >tel.: +39(02)574303355 >e-mail: davide.cittaro at ifom-ieo-campus.it >*/ > > > From davide.cittaro at ifom-ieo-campus.it Fri Aug 11 03:43:24 2006 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Fri, 11 Aug 2006 09:43:24 +0200 Subject: [Biococoa-dev] Reading blast formatted files In-Reply-To: <29348260.1155227673048.JavaMail.root@elwamui-lapwing.atl.sa.earthlink.net> References: <29348260.1155227673048.JavaMail.root@elwamui-lapwing.atl.sa.earthlink.net> Message-ID: Hi Koen On Aug 10, 2006, at 6:34 PM, Koen van der Drift wrote: > Hi Davide, > > Welcome to BioCocoa! It would be great if the framework will be > used in a proteomics app. Well, I have some ideas but, as I said, I'm pretty new to Cocoa programming, so you have to give me time to understand a lot of things... :-) > What I understand, formatdb is a standalone CLI app, correct? We > need to look into if we can add this (because of possible license > issues). Otherwise, we can write our own class, based on the > formatdb source code. I encourage you to look into that > possibility, we can help here to convert it to Objective-C and Cocoa. I'm thinking about reading the code of fastacmd utility instead of formatdb, as fastacmd does read blast formatted databases and can extract some info (whole sequences, accession numbers only, get only a sequence or the entire database...). I'll take a look then to the source code, then d > > cheers, > > - Koen. > > > > -----Original Message----- >> From: Davide Cittaro >> Sent: Aug 10, 2006 11:32 AM >> To: BioCocoa Mailinglist >> Subject: [Biococoa-dev] Reading blast formatted files >> >> Hi there, I'm new to BioCocoa (well, I've discovered it yesterday) >> and pretty new to Cocoa programming. I would like to start using this >> framework for some proteomics app. >> I would like to know if there is a way to read database formatted for >> NCBI blast with formatdb. Ok, I'm also going to read the >> documentation! >> >> d >> /* >> Davide Cittaro >> HPC and Bioinformatics Systems @ Informatics Core >> >> IFOM - Istituto FIRC di Oncologia Molecolare >> via adamello, 16 >> 20139 Milano >> Italy >> >> tel.: +39(02)574303355 >> e-mail: davide.cittaro at ifom-ieo-campus.it >> */ >> >> >> > > > /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303355 e-mail: davide.cittaro at ifom-ieo-campus.it */ -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Fri Aug 11 06:18:19 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 11 Aug 2006 06:18:19 -0400 Subject: [Biococoa-dev] Reading blast formatted files In-Reply-To: References: <29348260.1155227673048.JavaMail.root@elwamui-lapwing.atl.sa.earthlink.net> Message-ID: <43DB826A-8296-438C-8EE6-66F45C67752F@earthlink.net> On Aug 11, 2006, at 3:43 AM, Davide Cittaro wrote: > I'm thinking about reading the code of fastacmd utility instead of > formatdb, as fastacmd does read blast formatted databases and can > extract some info (whole sequences, accession numbers only, get > only a sequence or the entire database...). I'll take a look then > to the source code, then > Davide, BioCocoa can read fasta files, even with multiple entries. But maybe blast formatted databases have a different format. Maybe you could point to an example file, so we can see how to implement it? - Koen. From davide.cittaro at ifom-ieo-campus.it Fri Aug 11 06:26:47 2006 From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro) Date: Fri, 11 Aug 2006 12:26:47 +0200 Subject: [Biococoa-dev] Reading blast formatted files In-Reply-To: <43DB826A-8296-438C-8EE6-66F45C67752F@earthlink.net> References: <29348260.1155227673048.JavaMail.root@elwamui-lapwing.atl.sa.earthlink.net> <43DB826A-8296-438C-8EE6-66F45C67752F@earthlink.net> Message-ID: On Aug 11, 2006, at 12:18 PM, Koen van der Drift wrote: > Davide, > > BioCocoa can read fasta files, even with multiple entries. But > maybe blast formatted databases have a different format. Maybe you > could point to an example file, so we can see how to implement it? Actually you can download some blast formatted db from NCBI ftp site (ftp://ftp.ncbi.nih.gov/blast/db). They are in binary format and indexed, I assume they are some kind of dictionary dumps, so that you can retrieve sequences with an accession number. I haven't checked NCBI docs and sources, yet :-( d /* Davide Cittaro HPC and Bioinformatics Systems @ Informatics Core IFOM - Istituto FIRC di Oncologia Molecolare via adamello, 16 20139 Milano Italy tel.: +39(02)574303355 e-mail: davide.cittaro at ifom-ieo-campus.it */ -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Fri Aug 11 07:37:49 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 11 Aug 2006 07:37:49 -0400 Subject: [Biococoa-dev] Reading blast formatted files In-Reply-To: References: <29348260.1155227673048.JavaMail.root@elwamui-lapwing.atl.sa.earthlink.net> <43DB826A-8296-438C-8EE6-66F45C67752F@earthlink.net> Message-ID: On Aug 11, 2006, at 6:26 AM, Davide Cittaro wrote: > They are in binary format and indexed, I assume they are some kind > of dictionary dumps, so that you can retrieve sequences with an > accession number. I haven't checked NCBI docs and sources, yet :-( It would be great if we could add that to BioCocoa. Could you look into the binary format, and how to convert that to readable text files? cheers, - Koen. From mekentosj at gmail.com Fri Aug 25 21:41:51 2006 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Sat, 26 Aug 2006 02:41:51 +0100 Subject: [Biococoa-dev] Fwd: Posters, Abstracts & Author Contacts Posted - http://www.apple.com/science/poster/ References: <676DA7D5-CD0C-4BBB-A6C0-5A04B5006620@apple.com> Message-ID: <350F59E9-3A76-4E04-8F3B-1EEB429D948D@gmail.com> Hi guys, The biococoa poster + abstract is now available on apple's science page... Cheers, Alex Ps. Peter and Phil, look who's starring on one of the pictures of apple's main science page (http://www.apple.com/science ;-) Begin forwarded message: > From: Robert Kehrer > Subject: Posters, Abstracts & Author Contacts Posted - http:// > www.apple.com/science/poster/ > > Thanks one last time for participating in the WWDC Scientific > Development Poster Session and I hope that the contacts made will > spur some great collaborations. > > As a courtesy I wanted to let you know that all the titles, > abstracts, author contact information and poster .pdfs are now live > at: > http://www.apple.com/science/poster/ > > We anticipate that the podcasts will be made available in the near > future. ********************************************************* ** 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 Claiming that the Macintosh is inferior to Windows because most people use Windows, is like saying that all other restaurants serve food that is inferior to McDonalds ********************************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From kvddrift at earthlink.net Sat Aug 26 09:06:05 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sat, 26 Aug 2006 09:06:05 -0400 Subject: [Biococoa-dev] Fwd: Posters, Abstracts & Author Contacts Posted - http://www.apple.com/science/poster/ In-Reply-To: <350F59E9-3A76-4E04-8F3B-1EEB429D948D@gmail.com> References: <676DA7D5-CD0C-4BBB-A6C0-5A04B5006620@apple.com> <350F59E9-3A76-4E04-8F3B-1EEB429D948D@gmail.com> Message-ID: Cool :) I'll add some links to our website this weekend. - Koen. On Aug 25, 2006, at 9:41 PM, Alexander Griekspoor wrote: > Hi guys, > > The biococoa poster + abstract is now available on apple's science > page... > Cheers, > Alex > > Ps. Peter and Phil, look who's starring on one of the pictures of > apple's main science page (http://www.apple.com/science ;-) > > > > Begin forwarded message: > >> From: Robert Kehrer >> Subject: Posters, Abstracts & Author Contacts Posted - http:// >> www.apple.com/science/poster/ >> >> Thanks one last time for participating in the WWDC Scientific >> Development Poster Session and I hope that the contacts made will >> spur some great collaborations. >> >> As a courtesy I wanted to let you know that all the titles, >> abstracts, author contact information and poster .pdfs are now >> live at: >> http://www.apple.com/science/poster/ >> >> We anticipate that the podcasts will be made available in the near >> future. > > > ********************************************************* > ** 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 > > Claiming that the Macintosh is inferior to Windows > because most people use Windows, is like saying > that all other restaurants serve food that is > inferior to McDonalds > > ********************************************************* > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev From kvddrift at earthlink.net Sun Aug 27 08:46:45 2006 From: kvddrift at earthlink.net (Koen van der Drift) Date: Sun, 27 Aug 2006 08:46:45 -0400 Subject: [Biococoa-dev] BioCocoa wiki page Message-ID: <67B48C0F-6650-4A51-8B83-DA7A0519B4F6@earthlink.net> Hi, I have added a section 'Applications' and 'Bios' to the wiki page. I have alread added some applications that I know of that use BioCocoa, feel free to add more. Also, you can add a small description of yourself in the Bios section. cheers, - Koen.