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URL: From comm1965_1971 at SIGNTRONIX.COM Fri Sep 19 21:25:36 2008 From: comm1965_1971 at SIGNTRONIX.COM (Nathan) Date: Fri, 19 Sep 2008 20:25:36 -0500 Subject: [Biococoa-dev] ***SPAM*** 10 secrets to good family night life. Message-ID: An HTML attachment was scrubbed... URL: From Carissa-schapraa at 301east.com Sat Sep 20 22:07:46 2008 From: Carissa-schapraa at 301east.com (Carissa) Date: Sun, 21 Sep 2008 11:07:46 +0900 Subject: [Biococoa-dev] ***SPAM*** Give her a taste of your long and hard malehood. Message-ID: <69384.390.177.450.623.1311906845.squirrel@301east.com> An HTML attachment was scrubbed... URL: From schristley at mac.com Mon Sep 22 13:23:10 2008 From: schristley at mac.com (Scott Christley) Date: Mon, 22 Sep 2008 10:23:10 -0700 Subject: [Biococoa-dev] documentation Message-ID: Hello All, I started working on cleaning up the HeaderDoc documentation for BCFoundation, I am in the process of going through the source code files and fixing the tags, but you can take a look at what I currently have here: http://www.bioinformatics.org/biococoa/Documentation/BCFoundation/index.html Any comments on layouts, fonts, color schemes, etc. are appreciated. I'm not an HTML guru and HeaderDoc is somewhat limited but I will tweak what I can. On a side note, I was able to generate a docset which could be loaded up in Xcode 3, it looks pretty much like the web pages above except embedded within the Xcode documentation window. However, I notice that Xcode has a problem with some links generated by HeaderDoc. But look for this in the future, nice because you can do easy searching. cheers Scott From akhudek at cs.uwaterloo.ca Mon Sep 22 16:47:35 2008 From: akhudek at cs.uwaterloo.ca (Alexander K. Hudek) Date: Mon, 22 Sep 2008 16:47:35 -0400 Subject: [Biococoa-dev] project alive? Message-ID: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I'm playing around with BioCocoa for an alignment visualization application. It appears the project is no longer under active development? Is there still interesting in continuing development? I'm very new to Objective-C and Cocoa, but I'm not opposed to helping out. I've already had to modify the sequence reader class to allow it to read sequences with gap characters, although I'm not sure if this was the intended use of SequenceReader. Also, it looks like BCSequenceAlignment is very far from being finished. Is this correct? Regards, Alex Alexander K. Hudek School of Computer Science, University of Waterloo 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada Phone: +1 519 888 4567 x37886 Fax: +1 519 885 1208 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkjYBGcACgkQAI69dtlP4E1AGQCfbibQzS7ND+crvBvS3Fd0XvQf QHIAn2CmkZqifAaUIX3wZ0RO0wg3maRr =utoz -----END PGP SIGNATURE----- From schristley at mac.com Mon Sep 22 17:07:16 2008 From: schristley at mac.com (Scott Christley) Date: Mon, 22 Sep 2008 14:07:16 -0700 Subject: [Biococoa-dev] project alive? In-Reply-To: References: Message-ID: <98D45685-88FE-4615-B9E2-84104245D674@mac.com> Hello Alex, Yes, the project is still alive; however, many of the original developers have moved on to other things (though they might still be lurking on the list), so there is not much active development. I've been putting in code related to my research, e.g. suffix arrays, plus I have a bunch of local modifications dealing with managing gene expression data. I've recently tried getting the documentation in order. I haven't used BCSequenceAlignment but from looking at the code, it doesn't look like much is there. Duplicating existing work on sequence alignment is probably not the best use of resources, better to add wrapper and handlers to BioCocoa for other tools. By alignment visualization, do you mean something like JalView which gives a graphical output of CLUSTAL? I'm happy to take any of your changes and merge them back into the source. cheers Scott On Sep 22, 2008, at 1:47 PM, Alexander K. Hudek wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > I'm playing around with BioCocoa for an alignment visualization > application. It appears the project is no longer under active > development? Is there still interesting in continuing development? I'm > very new to Objective-C and Cocoa, but I'm not opposed to helping out. > > I've already had to modify the sequence reader class to allow it to > read sequences with gap characters, although I'm not sure if this was > the intended use of SequenceReader. Also, it looks like > BCSequenceAlignment is very far from being finished. Is this correct? > > Regards, > > Alex > > Alexander K. Hudek > School of Computer Science, University of Waterloo > 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada > Phone: +1 519 888 4567 x37886 Fax: +1 519 885 1208 > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.8 (Darwin) > > iEYEARECAAYFAkjYBGcACgkQAI69dtlP4E1AGQCfbibQzS7ND+crvBvS3Fd0XvQf > QHIAn2CmkZqifAaUIX3wZ0RO0wg3maRr > =utoz > -----END PGP SIGNATURE----- > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/biococoa-dev From mekentosj at gmail.com Mon Sep 22 17:13:16 2008 From: mekentosj at gmail.com (Alexander Griekspoor) Date: Mon, 22 Sep 2008 22:13:16 +0100 Subject: [Biococoa-dev] project alive? In-Reply-To: <98D45685-88FE-4615-B9E2-84104245D674@mac.com> References: <98D45685-88FE-4615-B9E2-84104245D674@mac.com> Message-ID: <8f2fa3f0809221413v6cbe6f7dyaddcd423d5c5faac@mail.gmail.com> Scott is right, most of all are still lurking around but unfortunately most of us who started the project have indeed moved on to different projects and/or have very little time. Scott is our current hope ;-) And of course it would be great to see new people take things up together with him to further develop the framework. Good luck! Alex On Mon, Sep 22, 2008 at 10:07 PM, Scott Christley wrote: > Hello Alex, > > Yes, the project is still alive; however, many of the original > developers have moved on to other things (though they might still be > lurking on the list), so there is not much active development. I've > been putting in code related to my research, e.g. suffix arrays, plus > I have a bunch of local modifications dealing with managing gene > expression data. I've recently tried getting the documentation in > order. > > I haven't used BCSequenceAlignment but from looking at the code, it > doesn't look like much is there. Duplicating existing work on > sequence alignment is probably not the best use of resources, better > to add wrapper and handlers to BioCocoa for other tools. > > By alignment visualization, do you mean something like JalView which > gives a graphical output of CLUSTAL? > > I'm happy to take any of your changes and merge them back into the > source. > > cheers > Scott > > On Sep 22, 2008, at 1:47 PM, Alexander K. Hudek wrote: > >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> I'm playing around with BioCocoa for an alignment visualization >> application. It appears the project is no longer under active >> development? Is there still interesting in continuing development? I'm >> very new to Objective-C and Cocoa, but I'm not opposed to helping out. >> >> I've already had to modify the sequence reader class to allow it to >> read sequences with gap characters, although I'm not sure if this was >> the intended use of SequenceReader. Also, it looks like >> BCSequenceAlignment is very far from being finished. Is this correct? >> >> Regards, >> >> Alex >> >> Alexander K. Hudek >> School of Computer Science, University of Waterloo >> 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada >> Phone: +1 519 888 4567 x37886 Fax: +1 519 885 1208 >> >> -----BEGIN PGP SIGNATURE----- >> Version: GnuPG v1.4.8 (Darwin) >> >> iEYEARECAAYFAkjYBGcACgkQAI69dtlP4E1AGQCfbibQzS7ND+crvBvS3Fd0XvQf >> QHIAn2CmkZqifAaUIX3wZ0RO0wg3maRr >> =utoz >> -----END PGP SIGNATURE----- >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/biococoa-dev > > > __________________________________________________ > D O T E A S Y - "Join the web hosting revolution!" > http://www.doteasy.com > -- **************************************************** ** Alexander Griekspoor PhD ** **************************************************** mekentosj.com Papers - Your Personal Library of Science 2007 Winner of the Apple Design Awards Best Mac OS X Scientific Solution http://www.mekentosj.com/papers **************************************************** From akhudek at cs.uwaterloo.ca Mon Sep 22 18:47:09 2008 From: akhudek at cs.uwaterloo.ca (Alexander K. Hudek) Date: Mon, 22 Sep 2008 18:47:09 -0400 Subject: [Biococoa-dev] project alive? In-Reply-To: <98D45685-88FE-4615-B9E2-84104245D674@mac.com> References: <98D45685-88FE-4615-B9E2-84104245D674@mac.com> Message-ID: I'm initially working on a slightly more flexible version of the Vista alignment tool (or similarly the SinicView tool) while I wait for research results to compute. This is in part to learn Cocoa programming and in part because I find both tools to be very clumsy and lacking in their ability to easily add custom annotation tracks. Ultimately, I'd like an easy to extend platform for both evaluating alignments and visualizing them in various ways. Too many of these sorts of tools are extremely customized to one particular data source. It isn't a major priority for me, but I figure that it's better to build functionality into a tool like this rather than create one shot command line tools as I've currently been doing. If I get somewhere useful with this, I'll be sure to send back changes and relevant classes. Regards, Alex On 2008-09-22, at 5:07 PM, Scott Christley wrote: > Hello Alex, > > Yes, the project is still alive; however, many of the original > developers have moved on to other things (though they might still be > lurking on the list), so there is not much active development. I've > been putting in code related to my research, e.g. suffix arrays, > plus I have a bunch of local modifications dealing with managing > gene expression data. I've recently tried getting the documentation > in order. > > I haven't used BCSequenceAlignment but from looking at the code, it > doesn't look like much is there. Duplicating existing work on > sequence alignment is probably not the best use of resources, better > to add wrapper and handlers to BioCocoa for other tools. > > By alignment visualization, do you mean something like JalView which > gives a graphical output of CLUSTAL? > > I'm happy to take any of your changes and merge them back into the > source. > > cheers > Scott > > On Sep 22, 2008, at 1:47 PM, Alexander K. Hudek wrote: > >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> I'm playing around with BioCocoa for an alignment visualization >> application. It appears the project is no longer under active >> development? Is there still interesting in continuing development? >> I'm >> very new to Objective-C and Cocoa, but I'm not opposed to helping >> out. >> >> I've already had to modify the sequence reader class to allow it to >> read sequences with gap characters, although I'm not sure if this was >> the intended use of SequenceReader. Also, it looks like >> BCSequenceAlignment is very far from being finished. Is this correct? >> >> Regards, >> >> Alex >> >> Alexander K. Hudek >> School of Computer Science, University of Waterloo >> 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada >> Phone: +1 519 888 4567 x37886 Fax: +1 519 885 1208 >> >> -----BEGIN PGP SIGNATURE----- >> Version: GnuPG v1.4.8 (Darwin) >> >> iEYEARECAAYFAkjYBGcACgkQAI69dtlP4E1AGQCfbibQzS7ND+crvBvS3Fd0XvQf >> QHIAn2CmkZqifAaUIX3wZ0RO0wg3maRr >> =utoz >> -----END PGP SIGNATURE----- >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev Alexander K. Hudek School of Computer Science, University of Waterloo 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada Phone: +1 519 888 4567 x37886 Fax: +1 519 885 1208 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PGP.sig Type: application/pgp-signature Size: 194 bytes Desc: This is a digitally signed message part URL: From kvddrift at earthlink.net Tue Sep 23 14:08:10 2008 From: kvddrift at earthlink.net (Koen van der Drift) Date: Tue, 23 Sep 2008 14:08:10 -0400 (GMT-04:00) Subject: [Biococoa-dev] project alive? Message-ID: <31181202.1222193290943.JavaMail.root@elwamui-huard.atl.sa.earthlink.net> Hi Alex, A slick sequence alignment tool would be the "Killer App" for BioCocoa! It would be great if you were able to use the framework for that. Annotations are still in an immature stage so that would need attention as well. As with some of the other original developers, I am also unable to spent much time on BioCocoa, but a fresh injection may change that. Welcome to the team, and if you'd like you can join the LinkedIn group. - Koen. -----Original Message----- >From: "Alexander K. Hudek" >Sent: Sep 22, 2008 6:47 PM >To: Scott Christley >Cc: biococoa-dev at bioinformatics.org >Subject: Re: [Biococoa-dev] project alive? > >I'm initially working on a slightly more flexible version of the Vista >alignment tool (or similarly the SinicView tool) while I wait for >research results to compute. This is in part to learn Cocoa >programming and in part because I find both tools to be very clumsy >and lacking in their ability to easily add custom annotation tracks. >Ultimately, I'd like an easy to extend platform for both evaluating >alignments and visualizing them in various ways. Too many of these >sorts of tools are extremely customized to one particular data source. > >It isn't a major priority for me, but I figure that it's better to >build functionality into a tool like this rather than create one shot >command line tools as I've currently been doing. If I get somewhere >useful with this, I'll be sure to send back changes and relevant >classes. > >Regards, > >Alex > >On 2008-09-22, at 5:07 PM, Scott Christley wrote: > >> Hello Alex, >> >> Yes, the project is still alive; however, many of the original >> developers have moved on to other things (though they might still be >> lurking on the list), so there is not much active development. I've >> been putting in code related to my research, e.g. suffix arrays, >> plus I have a bunch of local modifications dealing with managing >> gene expression data. I've recently tried getting the documentation >> in order. >> >> I haven't used BCSequenceAlignment but from looking at the code, it >> doesn't look like much is there. Duplicating existing work on >> sequence alignment is probably not the best use of resources, better >> to add wrapper and handlers to BioCocoa for other tools. >> >> By alignment visualization, do you mean something like JalView which >> gives a graphical output of CLUSTAL? >> >> I'm happy to take any of your changes and merge them back into the >> source. >> >> cheers >> Scott >> >> On Sep 22, 2008, at 1:47 PM, Alexander K. Hudek wrote: >> >>> -----BEGIN PGP SIGNED MESSAGE----- >>> Hash: SHA1 >>> >>> I'm playing around with BioCocoa for an alignment visualization >>> application. It appears the project is no longer under active >>> development? Is there still interesting in continuing development? >>> I'm >>> very new to Objective-C and Cocoa, but I'm not opposed to helping >>> out. >>> >>> I've already had to modify the sequence reader class to allow it to >>> read sequences with gap characters, although I'm not sure if this was >>> the intended use of SequenceReader. Also, it looks like >>> BCSequenceAlignment is very far from being finished. Is this correct? >>> >>> Regards, >>> >>> Alex >>> >>> Alexander K. Hudek >>> School of Computer Science, University of Waterloo >>> 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada >>> Phone: +1 519 888 4567 x37886 Fax: +1 519 885 1208 >>> >>> -----BEGIN PGP SIGNATURE----- >>> Version: GnuPG v1.4.8 (Darwin) >>> >>> iEYEARECAAYFAkjYBGcACgkQAI69dtlP4E1AGQCfbibQzS7ND+crvBvS3Fd0XvQf >>> QHIAn2CmkZqifAaUIX3wZ0RO0wg3maRr >>> =utoz >>> -----END PGP SIGNATURE----- >>> >>> _______________________________________________ >>> Biococoa-dev mailing list >>> Biococoa-dev at bioinformatics.org >>> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev > >Alexander K. Hudek >School of Computer Science, University of Waterloo >200 University Avenue West, Waterloo, ON, N2L 3G1, Canada >Phone: +1 519 888 4567 x37886 Fax: +1 519 885 1208 > From sdlohlit_1993 at NWDRIVE.COM Wed Sep 24 14:38:56 2008 From: sdlohlit_1993 at NWDRIVE.COM (corralie) Date: Wed, 24 Sep 2008 15:38:56 -0300 Subject: [Biococoa-dev] ***SPAM*** 9 Things You Can Do Right Now To Boost Your Happiness Message-ID: <77476.834.185.861.928.1341212883.squirrel@NWDRIVE.COM> An HTML attachment was scrubbed... URL: From Izooba-emjiwzeb at Kotting-Uhl.de Thu Sep 25 19:08:11 2008 From: Izooba-emjiwzeb at Kotting-Uhl.de (Izooba) Date: Thu, 25 Sep 2008 19:08:11 -0400 Subject: [Biococoa-dev] ***SPAM*** Strenghth and power for you. Message-ID: <80193.206.915.161.128.1145931752.squirrel@Kotting-Uhl.de> An HTML attachment was scrubbed... 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URL: From Moishe-gpnp at 7point4.biz Sat Sep 27 20:18:34 2008 From: Moishe-gpnp at 7point4.biz (Moishe) Date: Sat, 27 Sep 2008 19:18:34 -0500 Subject: [Biococoa-dev] ***SPAM*** All Meds are onsale Today Come see our closeout prices Message-ID: <000501c920ff$bea714e0$9a45f84a@SONY> This message was sent to biococoa-dev at bioinformatics.org Unsubscribe | Manage Subscriptions | Privacy Policy To stop ALL email from CPA Newsletters, click here to remove yourself from our lists. This email was sent by: CPA, 524 W. 57th St., Room 514/1, New York, NY, 10019 2008 CPA -------------- next part -------------- An HTML attachment was scrubbed... URL: From Triet-netsytyv at CVALLEY.NET Sat Sep 27 21:29:59 2008 From: Triet-netsytyv at CVALLEY.NET (Triet) Date: Sat, 27 Sep 2008 21:29:59 -0400 Subject: [Biococoa-dev] ***SPAM*** Amase your gf with your new hard and rock rod Message-ID: <000701c92109$b8a03860$4141f248@cyndi> This message was sent to biococoa-dev at bioinformatics.org Unsubscribe | Manage Subscriptions | Privacy Policy To stop ALL email from CPA Newsletters, click here to remove yourself from our lists. This email was sent by: CPA, 524 W. 57th St., Room 514/1, New York, NY, 10019 2008 CPA -------------- next part -------------- An HTML attachment was scrubbed... URL: From elve_1970 at HILLCRESTFORD.COM Sun Sep 28 20:09:15 2008 From: elve_1970 at HILLCRESTFORD.COM (hasmet) Date: Sun, 28 Sep 2008 17:09:15 -0700 Subject: [Biococoa-dev] ***SPAM*** Be proud of your masculin symbol Message-ID: <000601c921c7$9c3494f0$2d119340@yourus67pi6luv> This message was sent to biococoa-dev at bioinformatics.org Unsubscribe | Manage Subscriptions | Privacy Policy To stop ALL email from CPA Newsletters, click here to remove yourself from our lists. This email was sent by: CPA, 524 W. 57th St., Room 514/1, New York, NY, 10019 2008 CPA -------------- next part -------------- An HTML attachment was scrubbed... URL: From otatclum at Bio-logic.com Mon Sep 29 10:08:13 2008 From: otatclum at Bio-logic.com (asmin) Date: Mon, 29 Sep 2008 16:08:13 +0200 Subject: [Biococoa-dev] ***SPAM*** We are would to offer you high quality medical products at the best cost in the market. Message-ID: <000501c9223c$cfe6ee90$87f91657@VAJOPAOLO> This message was sent to biococoa-dev at bioinformatics.org Unsubscribe | Manage Subscriptions | Privacy Policy To stop ALL email from CPA Newsletters, click here to remove yourself from our lists. This email was sent by: CPA, 524 W. 57th St., Room 514/1, New York, NY, 10019 2008 CPA -------------- next part -------------- An HTML attachment was scrubbed... URL: From sjektere1976 at MedcoSupply.com Mon Sep 29 11:54:37 2008 From: sjektere1976 at MedcoSupply.com (Rexelle) Date: Mon, 29 Sep 2008 17:54:37 +0200 Subject: [Biococoa-dev] ***SPAM*** The Internet Drug Index for prescription drugs Message-ID: <000301c9224b$acd87bd0$97036a52@daeasti> This message was sent to biococoa-dev at bioinformatics.org Unsubscribe | Manage Subscriptions | Privacy Policy To stop ALL email from CPA Newsletters, click here to remove yourself from our lists. This email was sent by: CPA, 524 W. 57th St., Room 514/1, New York, NY, 10019 2008 CPA -------------- next part -------------- An HTML attachment was scrubbed... URL: From kaoserp at 2cjc.com Mon Sep 29 22:28:38 2008 From: kaoserp at 2cjc.com (Beau) Date: Tue, 30 Sep 2008 04:28:38 +0200 Subject: [Biococoa-dev] ***SPAM*** We strive to meet every one of your pharmaceutical needs Message-ID: <000c01c922a4$3f44e370$5e30ead4@pcdirection> This message was sent to biococoa-dev at bioinformatics.org Unsubscribe | Manage Subscriptions | Privacy Policy To stop ALL email from CPA Newsletters, click here to remove yourself from our lists. This email was sent by: CPA, 524 W. 57th St., Room 514/1, New York, NY, 10019 2008 CPA -------------- next part -------------- An HTML attachment was scrubbed... URL: From Padam-segtaaga at tartanfields.com Mon Sep 29 23:49:16 2008 From: Padam-segtaaga at tartanfields.com (Padam) Date: Tue, 30 Sep 2008 10:49:16 +0700 Subject: [Biococoa-dev] ***SPAM*** your one-stop destination for affordable high-quality med|c@tionz Message-ID: <000e01c922af$82e840d0$4e3e98ca@Contruction> This message was sent to biococoa-dev at bioinformatics.org Unsubscribe | Manage Subscriptions | Privacy Policy To stop ALL email from CPA Newsletters, click here to remove yourself from our lists. This email was sent by: CPA, 524 W. 57th St., Room 514/1, New York, NY, 10019 2008 CPA -------------- next part -------------- An HTML attachment was scrubbed... URL: From scott.christley at uci.edu Tue Sep 30 14:01:48 2008 From: scott.christley at uci.edu (Scott Christley) Date: Tue, 30 Sep 2008 11:01:48 -0700 Subject: [Biococoa-dev] new release? Message-ID: <540DACE7-C595-4202-9E3D-DA9878562E0B@uci.edu> Hello All, I would like to put together a new release of BioCocoa. I've started the process to get BioCocoa packaged into downstream Linux distributions like Debian, Ubuntu and Fedora. Though this will take some time, having a new release will help out testing of the packaging. There is still work to be done on the GNUstep/Linux side of things, but mostly this is figuring out Cocoa'isms (documentation, test suite), the BCFoundation functionality appears to be working well. This will also alleviate some users wanting to use the ultraconserved application I published, which currently requires them to compile the source code from SVN. Any suggestions, comments? I'm gonna do a walk-through of the whole release process, then write up a wiki page with the steps. cheers Scott From charles.parnot at gmail.com Tue Sep 30 14:19:22 2008 From: charles.parnot at gmail.com (Charles Parnot) Date: Tue, 30 Sep 2008 11:19:22 -0700 Subject: [Biococoa-dev] new release? In-Reply-To: <540DACE7-C595-4202-9E3D-DA9878562E0B@uci.edu> References: <540DACE7-C595-4202-9E3D-DA9878562E0B@uci.edu> Message-ID: > I'm gonna do a walk-through of the whole release process, then write > up a wiki page with the steps. Thanks, Scott, that is awesome, I am really glad somebody is stepping up the plate. My 2 cents :-) charles -- OpenMacGrid Help science move fast forward: http://www.macresearch.org/openmacgrid Charles Parnot charles.parnot at gmail.com