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URL: From Svetoslav-sgnitnir at KAFIGROUP.COM Wed Jul 9 01:32:16 2008 From: Svetoslav-sgnitnir at KAFIGROUP.COM (Nikoula) Date: Wed, 9 Jul 2008 07:32:16 +0200 Subject: [Biococoa-dev] ***SPAM*** Coming of Great Depression II Message-ID: Everyone on the team scores when her pom-poms fly http://www.wellhave.com/ -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From edsoolet_1972 at ctgcorp.com Wed Jul 9 08:33:55 2008 From: edsoolet_1972 at ctgcorp.com (Covintree) Date: Wed, 9 Jul 2008 14:33:55 +0200 Subject: [Biococoa-dev] ***SPAM*** Coming of Great Depression II Message-ID: You've heard about the lindsay sucking video; here's the link to view all 20 minutes of blowing action. http://www.tiptall.com/ -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From ijkkrvni_2002 at 1stlg.com Thu Jul 10 03:42:53 2008 From: ijkkrvni_2002 at 1stlg.com (Callie) Date: Thu, 10 Jul 2008 02:42:53 -0500 Subject: [Biococoa-dev] The latest developments in medical science Message-ID: Watch her come over and over again, and moan louder than ever before with this. http://www.galestem.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From Robet-kymmenys at silvey.co.uk Thu Jul 10 20:28:07 2008 From: Robet-kymmenys at silvey.co.uk (Robet) Date: Fri, 11 Jul 2008 09:28:07 +0900 Subject: [Biococoa-dev] Get your pole bigger today Message-ID: Stop being fooled by the imitators, get the real thing here http://www.willline.com/ -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From aonemell2005 at sblhs.org Fri Jul 11 12:21:05 2008 From: aonemell2005 at sblhs.org (robins) Date: Fri, 11 Jul 2008 18:21:05 +0200 Subject: [Biococoa-dev] Tom Cruise killed in plane crash Message-ID: Bring more happiness to your lady in bed, visit out website to find out how http://www.stemmind.com/ -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From Bennie-rbanisez at sunterra.com Fri Jul 11 13:51:42 2008 From: Bennie-rbanisez at sunterra.com (Dore) Date: Fri, 11 Jul 2008 12:51:42 -0500 Subject: [Biococoa-dev] ***SPAM*** Iranian missile tests cause worldwide panic Message-ID: You will find it much harder to get rid of your one night stand once you have grown an extra inch http://www.makestem.com/ -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From aitaukse at traxdata.com Mon Jul 14 05:01:44 2008 From: aitaukse at traxdata.com (persad) Date: Mon, 14 Jul 2008 11:01:44 +0200 Subject: [Biococoa-dev] ***SPAM*** American hostages beheaded in Colombia Message-ID: Gay marriages legalised in US Senate, homosexuals rejoice http://s147318022.onlinehome.fr/main.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From paolo_siniselli at yahoo.it Mon Jul 14 17:06:22 2008 From: paolo_siniselli at yahoo.it (paolo siniselli) Date: Mon, 14 Jul 2008 21:06:22 +0000 (GMT) Subject: [Biococoa-dev] Biococoa2 Install issue Message-ID: <205459.61845.qm@web26706.mail.ukl.yahoo.com> I'm trying to install BioCocoa2 on my Linux Debian (Lenny) I've already installed GNUstep So I went into truck/GNUstep folder and I typed "make install" but I received an error back: GNUmakefile:27: *** You need to run the GNUstep configuration script before compiling!.? Stop. Those are the files in GNUstep directory: aminoacids.plist? GNUmakefile.postamble? GNUmakefile.subproj GNUmakefile?????? GNUmakefile.preamble?? nucleotides.plist And those are the file in truck direcotry: BCAppKit?????????? BioCocoa.xcodeproj? Examples???? Publications.txt BCFoundation?????? Copying.txt???????? GNUstep????? Readme.txt BC.icns??????????? DeveloperDocs?????? license.txt? Resources BioCocoa_Prefix.h? Documentation?????? main.c?????? Tests Thanks Paolo Posta, news, sport, oroscopo: tutto in una sola pagina. Crea l'home page che piace a te! www.yahoo.it/latuapagina -------------- next part -------------- An HTML attachment was scrubbed... URL: From schristley at mac.com Mon Jul 14 17:27:08 2008 From: schristley at mac.com (Scott Christley) Date: Mon, 14 Jul 2008 14:27:08 -0700 Subject: [Biococoa-dev] Biococoa2 Install issue In-Reply-To: <205459.61845.qm@web26706.mail.ukl.yahoo.com> References: <205459.61845.qm@web26706.mail.ukl.yahoo.com> Message-ID: <0E7DDE91-47C5-4999-9977-A92281969048@mac.com> Hello Paolo, There is an environment configuration script that comes with GNUstep, you need to "source" this script to setup the GNUstep environment before compiling or running applications. Maybe something like this: . /usr/share/GNUstep/Makefiles/GNUstep.sh As a side note, some of the reports I've heard from people is that the GNUstep which comes with Debian is old and has bugs, I cannot say how well it will work with BioCocoa. cheers Scott On Jul 14, 2008, at 2:06 PM, paolo siniselli wrote: > I'm trying to install BioCocoa2 on my Linux Debian (Lenny) > I've already installed GNUstep > So I went into truck/GNUstep folder and I typed "make install" but I > received an error back: > GNUmakefile:27: *** You need to run the GNUstep configuration script > before compiling!. Stop. > > Those are the files in GNUstep directory: > aminoacids.plist GNUmakefile.postamble GNUmakefile.subproj > GNUmakefile GNUmakefile.preamble nucleotides.plist > > And those are the file in truck direcotry: > BCAppKit BioCocoa.xcodeproj Examples Publications.txt > BCFoundation Copying.txt GNUstep Readme.txt > BC.icns DeveloperDocs license.txt Resources > BioCocoa_Prefix.h Documentation main.c Tests > > Thanks > Paolo > > Posta, news, sport, oroscopo: tutto in una sola pagina > Crea l'home page che piace a > te!._______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/biococoa-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From miso-nmereivn at aroxy.com Tue Jul 15 11:43:49 2008 From: miso-nmereivn at aroxy.com (miso) Date: Tue, 15 Jul 2008 10:43:49 -0500 Subject: [Biococoa-dev] [SPAM+] Old man grabs young boobies Message-ID: Tanning lamps linked to skin damage, freckles and cancer in latest healthcare scare http://pepinieres-de-beaufort.com/main.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From gustiest2007 at stanleyus.com Tue Jul 15 20:13:22 2008 From: gustiest2007 at stanleyus.com (DAndrea) Date: Wed, 16 Jul 2008 02:13:22 +0200 Subject: [Biococoa-dev] Geek turns into hot babe Message-ID: Solar energy - new breakthrough for power http://sattelmessungen.de/about.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From dori-rstrozen at eads.com.br Wed Jul 16 02:06:31 2008 From: dori-rstrozen at eads.com.br (Smalls) Date: Wed, 16 Jul 2008 03:06:31 -0300 Subject: [Biococoa-dev] Muhammad Ali dies at 71 Message-ID: <9EC34C63-D15E-6669-593E-2948440485F9@eads.com.br> You will not believe your eyes, look at the size of that thing http://aacademia.com/about.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From paolo_siniselli at yahoo.it Wed Jul 16 17:40:13 2008 From: paolo_siniselli at yahoo.it (paolo siniselli) Date: Wed, 16 Jul 2008 21:40:13 +0000 (GMT) Subject: [Biococoa-dev] ultraconserved sarray info In-Reply-To: <0E7DDE91-47C5-4999-9977-A92281969048@mac.com> Message-ID: <376184.93678.qm@web26704.mail.ukl.yahoo.com> Hi Scott, How can I combine all the suffix array files for an organism into a single suffix array so that mcp_sarray is just run once? I'd like to compare two sarray files for each two organisms comparison such as human vs mouse... thanks --- Lun 14/7/08, Scott Christley ha scritto: Da: Scott Christley Oggetto: Re: [Biococoa-dev] Biococoa2 Install issue A: paolo_siniselli at yahoo.it Cc: "biococoa" Data: Luned? 14 luglio 2008, 23:27 Hello Paolo, There is an environment configuration script that comes with GNUstep, you need to "source" this script to setup the GNUstep environment before compiling or running applications. ?Maybe something like this: . /usr/share/GNUstep/Makefiles/GNUstep.sh As a side note, some of the reports I've heard from people is that the GNUstep which comes with Debian is old and has bugs, I cannot say how well it will work with BioCocoa. cheersScott On Jul 14, 2008, at 2:06 PM, paolo siniselli wrote: I'm trying to install BioCocoa2 on my Linux Debian (Lenny) I've already installed GNUstep So I went into truck/GNUstep folder and I typed "make install" but I received an error back: GNUmakefile:27: *** You need to run the GNUstep configuration script before compiling!.? Stop. Those are the files in GNUstep directory: aminoacids.plist? GNUmakefile.postamble? GNUmakefile.subproj GNUmakefile?????? GNUmakefile.preamble?? nucleotides.plist And those are the file in truck direcotry: BCAppKit?????????? BioCocoa.xcodeproj? Examples???? Publications.txt BCFoundation?????? Copying.txt???????? GNUstep????? Readme.txt BC.icns??????????? DeveloperDocs?????? license.txt? Resources BioCocoa_Prefix.h? Documentation?????? main.c?????? Tests Thanks Paolo Posta, news, sport, oroscopo: tutto in una sola pagina Crea l'home page che piace a te!._______________________________________________ Biococoa-dev mailing list Biococoa-dev at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/biococoa-dev Posta, news, sport, oroscopo: tutto in una sola pagina. Crea l'home page che piace a te! www.yahoo.it/latuapagina -------------- next part -------------- An HTML attachment was scrubbed... URL: From schristley at mac.com Wed Jul 16 21:18:16 2008 From: schristley at mac.com (Scott Christley) Date: Wed, 16 Jul 2008 18:18:16 -0700 Subject: [Biococoa-dev] ultraconserved sarray info In-Reply-To: <376184.93678.qm@web26704.mail.ukl.yahoo.com> References: <376184.93678.qm@web26704.mail.ukl.yahoo.com> Message-ID: <6D90D83D-E1F1-4052-B8DE-8431BFDFB65C@mac.com> Hello Paolo, When originally designing the programs, my thought was similar to this, combine all of the suffix arrays together. Unfortunately this is not very efficient, it takes a long time to combine those suffix arrays and it produces a very very large file as you can imagine. Also, one of my design goals was to be able to split the work across multiple machines, with a single file you are limited to using just one machine. So what I did instead is to union the results of mcp_sarray, this is the union_mcp command. Later though, I did find a need to combine suffix arrays however only programmatically, I never wrote a command line program. This is using the BCSuffixArrayUnionEnumerator. Anyways, what I did in my work was to write a shell script to loop through all the chromosome files, such as this: # i is mouse chromosomes # j is human chromosomes for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X Y; do for j in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y; do mcp_sarray N human_chr${j} mouse_chr${i} h${j}_m${i} 40 done done I actually did something a little more complicated than this because I distributed the work across a cluster of machines. However, this will produce result files with hA_mB where A and B are chromosome numbers, then you can use another script to combine all of them together to produce a single result. # i is mouse chromosomes # j is human chromosomes union_mcp h1_m1 h2_m1 hm_1 L=1 K=2 for j in 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y; do union_mcp hm_${L} h${j}_m1 hm_${K} K=$((K + 1)) L=$((L + 1)) done for i in 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X Y; do for j in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y; do union_mcp hm_${L} h${j}_m${i} hm_${K} K=$((K + 1)) L=$((L + 1)) done done This produces files hm_K where K is an increasing number. The file with the largest K at the end is your final result file. cheers Scott On Jul 16, 2008, at 2:40 PM, paolo siniselli wrote: > Hi Scott, > How can I combine all the suffix array files for an organism into a > single suffix array so that mcp_sarray is just run once? > I'd like to compare two sarray files for each two organisms > comparison such as human vs mouse... > thanks > > > > --- Lun 14/7/08, Scott Christley ha scritto: > Da: Scott Christley > Oggetto: Re: [Biococoa-dev] Biococoa2 Install issue > A: paolo_siniselli at yahoo.it > Cc: "biococoa" > Data: Luned? 14 luglio 2008, 23:27 > > Hello Paolo, > > There is an environment configuration script that comes with > GNUstep, you need to "source" this script to setup the GNUstep > environment before compiling or running applications. Maybe > something like this: > > . /usr/share/GNUstep/Makefiles/GNUstep.sh > > As a side note, some of the reports I've heard from people is that > the GNUstep which comes with Debian is old and has bugs, I cannot > say how well it will work with BioCocoa. > > cheers > Scott > > > On Jul 14, 2008, at 2:06 PM, paolo siniselli wrote: > >> I'm trying to install BioCocoa2 on my Linux Debian (Lenny) >> I've already installed GNUstep >> So I went into truck/GNUstep folder and I typed "make install" but >> I received an error back: >> GNUmakefile:27: *** You need to run the GNUstep configuration >> script before compiling!. Stop. >> >> Those are the files in GNUstep directory: >> aminoacids.plist GNUmakefile.postamble GNUmakefile.subproj >> GNUmakefile GNUmakefile.preamble nucleotides.plist >> >> And those are the file in truck direcotry: >> BCAppKit BioCocoa.xcodeproj Examples Publications.txt >> BCFoundation Copying.txt GNUstep Readme.txt >> BC.icns DeveloperDocs license.txt Resources >> BioCocoa_Prefix.h Documentation main.c Tests >> >> Thanks >> Paolo >> >> Posta, news, sport, oroscopo: tutto in una sola pagina >> Crea l'home page che piace a >> te!._______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev > > > Posta, news, sport, oroscopo: tutto in una sola pagina > Crea l'home page che piace a te!. -------------- next part -------------- An HTML attachment was scrubbed... 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URL: From paolo_siniselli at yahoo.it Mon Jul 21 16:24:21 2008 From: paolo_siniselli at yahoo.it (paolo siniselli) Date: Mon, 21 Jul 2008 20:24:21 +0000 (GMT) Subject: [Biococoa-dev] ultraconserved tools bugged? Message-ID: <18370.66320.qm@web26702.mail.ukl.yahoo.com> Hi Schott, I used construct_sarray to create an sarray file from the human genome It worked great, but when I tried to do the same using a bacteria or virus genome, it didn't work at all. It says? "Constructing suffix array. Aborted" Do your tools work with small genomes? For example one of these (http://www.ebi.ac.uk/genomes/virus.html) Let me know Thanks p. Posta, news, sport, oroscopo: tutto in una sola pagina. Crea l'home page che piace a te! www.yahoo.it/latuapagina -------------- next part -------------- An HTML attachment was scrubbed... URL: From taruk_2005 at ascr.com Tue Jul 22 01:58:36 2008 From: taruk_2005 at ascr.com (Loralea) Date: Tue, 22 Jul 2008 07:58:36 +0200 Subject: [Biococoa-dev] Cristiano Ronaldo Disses Paris Hilton "um Louro Mudo Feio!" Message-ID: Gus Hiddink Heads For Gulag http://leonardodavi.com/viewmovie.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From orloofde at cable-lynx.net Tue Jul 22 07:14:30 2008 From: orloofde at cable-lynx.net (Boily) Date: Tue, 22 Jul 2008 06:14:30 -0500 Subject: [Biococoa-dev] Kids leave robbery victim dead Message-ID: <000301c8ebec$1c8b2770$fe77ac4a@HPComputer> Swiss youth kills classmate in canteen stabbing http://overunity.it/viewmovie.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From nagirrac at meinerscatering.com Tue Jul 22 13:19:26 2008 From: nagirrac at meinerscatering.com (Fassett) Date: Tue, 22 Jul 2008 13:19:26 -0400 Subject: [Biococoa-dev] ***SPAM*** Great things come in huge sizes Message-ID: The miraculous herbal supplement helps maintain erection longer and heighten your orgasms http://www.genrace.com/ -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From aduttori_2006 at seattlearch.org Fri Jul 25 03:45:40 2008 From: aduttori_2006 at seattlearch.org (Jatinderpal) Date: Fri, 25 Jul 2008 17:45:40 +1000 Subject: [Biococoa-dev] Thugs piss on corpses Message-ID: <3EAA80C9.F49914FE@seattlearch.org> The day the sky turned green, the explanation right here. http://www.slawa.hg.pl/watchit.html From schristley at mac.com Fri Jul 25 14:21:19 2008 From: schristley at mac.com (Scott Christley) Date: Fri, 25 Jul 2008 11:21:19 -0700 Subject: [Biococoa-dev] #pragma mark and headerdoc2html Message-ID: Has anybody noticed that using the #pragma mark to give nice little section titles in Xcode cause headerdoc2html to not work properly? 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