From schristley at mac.com Tue Mar 1 17:31:29 2011 From: schristley at mac.com (Scott Christley) Date: Tue, 01 Mar 2011 16:31:29 -0600 Subject: [Biococoa-dev] some BioCocoa news Message-ID: <6B76BD27-3B63-4B5F-8A22-83A8353B0EFB@mac.com> Hello All, Here is some news about BioCocoa. * BioCocoa has now been packaged for the Debian (and Ubuntu) operating systems by the Debian-Med[1] team. This means that users can use the standard Debian packaging system to easily install a pre-built version of BioCocoa along with its dependencies (GNUstep mainly). It should make it in the next major release of Debian but is currently available in the "unstable" and "testing" distributions [2]. * There has been a number of new classes added to BioCocoa including BCParseOBO (reads ontology files in OBO format), BCBioPortalREST (download ontologies from the BioPortal web site), and a cluster of classes for reading compound, reaction and model databases for genome-scale metabolic models. The classes for metabolic models are being designed to interface with Argonne's SEED system [3]. * The BioSwarm framework has been added to BioCocoa SVN repository. BioSwarm is an OpenStep framework for computational biological modeling and simulation. It provides a suite of capabilities including gene network inference, flux-balance analysis for genome-scale metabolic models, classes for advanced spatial biological modeling, and GPU tools for running massively parallel simulations. BioSwarm includes much of the research that I've been doing for biological modeling, and I've made it public as I'm starting to gain a few users of the software. Plus I included it alongside BioCocoa because I think it is a complementary framework. * The BioCocoa wiki [4] has undergone some re-organization, check it out! cheers Scott [1] http://www.debian.org/devel/debian-med [2] http://packages.debian.org/search?keywords=libbiococoa [3] http://www.theseed.org/wiki/Main_Page [4] http://www.bioinformatics.org/biococoa/wiki/pmwiki.php From charles.parnot at gmail.com Tue Mar 1 18:25:01 2011 From: charles.parnot at gmail.com (Charles Parnot) Date: Tue, 1 Mar 2011 15:25:01 -0800 Subject: [Biococoa-dev] some BioCocoa news In-Reply-To: <6B76BD27-3B63-4B5F-8A22-83A8353B0EFB@mac.com> References: <6B76BD27-3B63-4B5F-8A22-83A8353B0EFB@mac.com> Message-ID: <7F49513D-1F3E-4965-89CA-581EDCB282D7@gmail.com> Wow, thanks for the update! I did not realize there was so much activity still going on :-) On Mar 1, 2011, at 2:31 PM, Scott Christley wrote: > Hello All, > > Here is some news about BioCocoa. > > * BioCocoa has now been packaged for the Debian (and Ubuntu) operating systems by the Debian-Med[1] team. This means that users can use the standard Debian packaging system to easily install a pre-built version of BioCocoa along with its dependencies (GNUstep mainly). It should make it in the next major release of Debian but is currently available in the "unstable" and "testing" distributions [2]. > > * There has been a number of new classes added to BioCocoa including BCParseOBO (reads ontology files in OBO format), BCBioPortalREST (download ontologies from the BioPortal web site), and a cluster of classes for reading compound, reaction and model databases for genome-scale metabolic models. The classes for metabolic models are being designed to interface with Argonne's SEED system [3]. > > * The BioSwarm framework has been added to BioCocoa SVN repository. BioSwarm is an OpenStep framework for computational biological modeling and simulation. It provides a suite of capabilities including gene network inference, flux-balance analysis for genome-scale metabolic models, classes for advanced spatial biological modeling, and GPU tools for running massively parallel simulations. BioSwarm includes much of the research that I've been doing for biological modeling, and I've made it public as I'm starting to gain a few users of the software. Plus I included it alongside BioCocoa because I think it is a complementary framework. > > * The BioCocoa wiki [4] has undergone some re-organization, check it out! > > cheers > Scott > > [1] http://www.debian.org/devel/debian-med > [2] http://packages.debian.org/search?keywords=libbiococoa > [3] http://www.theseed.org/wiki/Main_Page > [4] http://www.bioinformatics.org/biococoa/wiki/pmwiki.php > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/biococoa-dev -- Charles Parnot charles.parnot at gmail.com twitter: @cparnot http://mekentosj.com From koenvanderdrift at gmail.com Tue Mar 1 20:50:30 2011 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Tue, 1 Mar 2011 20:50:30 -0500 Subject: [Biococoa-dev] some BioCocoa news In-Reply-To: <7F49513D-1F3E-4965-89CA-581EDCB282D7@gmail.com> References: <6B76BD27-3B63-4B5F-8A22-83A8353B0EFB@mac.com> <7F49513D-1F3E-4965-89CA-581EDCB282D7@gmail.com> Message-ID: <81EC4A12-948C-4568-98A4-41F04C5BA989@gmail.com> That's indeed great to hear. Thanks for keeping the BioCocoa project alive, Scott. - Koen. On Mar 1, 2011, at 6:25 PM, Charles Parnot wrote: > Wow, thanks for the update! I did not realize there was so much activity still going on :-) > > > On Mar 1, 2011, at 2:31 PM, Scott Christley wrote: > >> Hello All, >> >> Here is some news about BioCocoa. >> >> * BioCocoa has now been packaged for the Debian (and Ubuntu) operating systems by the Debian-Med[1] team. This means that users can use the standard Debian packaging system to easily install a pre-built version of BioCocoa along with its dependencies (GNUstep mainly). It should make it in the next major release of Debian but is currently available in the "unstable" and "testing" distributions [2]. >> >> * There has been a number of new classes added to BioCocoa including BCParseOBO (reads ontology files in OBO format), BCBioPortalREST (download ontologies from the BioPortal web site), and a cluster of classes for reading compound, reaction and model databases for genome-scale metabolic models. The classes for metabolic models are being designed to interface with Argonne's SEED system [3]. >> >> * The BioSwarm framework has been added to BioCocoa SVN repository. BioSwarm is an OpenStep framework for computational biological modeling and simulation. It provides a suite of capabilities including gene network inference, flux-balance analysis for genome-scale metabolic models, classes for advanced spatial biological modeling, and GPU tools for running massively parallel simulations. BioSwarm includes much of the research that I've been doing for biological modeling, and I've made it public as I'm starting to gain a few users of the software. Plus I included it alongside BioCocoa because I think it is a complementary framework. >> >> * The BioCocoa wiki [4] has undergone some re-organization, check it out! >> >> cheers >> Scott >> >> [1] http://www.debian.org/devel/debian-med >> [2] http://packages.debian.org/search?keywords=libbiococoa >> [3] http://www.theseed.org/wiki/Main_Page >> [4] http://www.bioinformatics.org/biococoa/wiki/pmwiki.php >> >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev > > -- > Charles Parnot > charles.parnot at gmail.com > twitter: @cparnot > http://mekentosj.com > > > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/biococoa-dev From koenvanderdrift at gmail.com Sat Mar 5 12:22:37 2011 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Sat, 5 Mar 2011 12:22:37 -0500 Subject: [Biococoa-dev] some BioCocoa news In-Reply-To: <7F49513D-1F3E-4965-89CA-581EDCB282D7@gmail.com> References: <6B76BD27-3B63-4B5F-8A22-83A8353B0EFB@mac.com> <7F49513D-1F3E-4965-89CA-581EDCB282D7@gmail.com> Message-ID: <5AD58156-2A06-4185-83D0-639FC75AAE84@gmail.com> Just for kicks, I downloaded the latest and greatest and tried to compile it. However, I get a missing file error BCParseGFF.h/.m - is this not yet added yet to the repository? Thanks, - Koen. On Mar 1, 2011, at 2:31 PM, Scott Christley wrote: > Hello All, > > Here is some news about BioCocoa. > > * BioCocoa has now been packaged for the Debian (and Ubuntu) operating systems by the Debian-Med[1] team. This means that users can use the standard Debian packaging system to easily install a pre-built version of BioCocoa along with its dependencies (GNUstep mainly). It should make it in the next major release of Debian but is currently available in the "unstable" and "testing" distributions [2]. > > * There has been a number of new classes added to BioCocoa including BCParseOBO (reads ontology files in OBO format), BCBioPortalREST (download ontologies from the BioPortal web site), and a cluster of classes for reading compound, reaction and model databases for genome-scale metabolic models. The classes for metabolic models are being designed to interface with Argonne's SEED system [3]. > > * The BioSwarm framework has been added to BioCocoa SVN repository. BioSwarm is an OpenStep framework for computational biological modeling and simulation. It provides a suite of capabilities including gene network inference, flux-balance analysis for genome-scale metabolic models, classes for advanced spatial biological modeling, and GPU tools for running massively parallel simulations. BioSwarm includes much of the research that I've been doing for biological modeling, and I've made it public as I'm starting to gain a few users of the software. Plus I included it alongside BioCocoa because I think it is a complementary framework. > > * The BioCocoa wiki [4] has undergone some re-organization, check it out! > > cheers > Scott > > [1] http://www.debian.org/devel/debian-med > [2] http://packages.debian.org/search?keywords=libbiococoa > [3] http://www.theseed.org/wiki/Main_Page > [4] http://www.bioinformatics.org/biococoa/wiki/pmwiki.php > >> From schristley at mac.com Sat Mar 5 12:28:47 2011 From: schristley at mac.com (Scott Christley) Date: Sat, 05 Mar 2011 11:28:47 -0600 Subject: [Biococoa-dev] some BioCocoa news In-Reply-To: <5AD58156-2A06-4185-83D0-639FC75AAE84@gmail.com> References: <6B76BD27-3B63-4B5F-8A22-83A8353B0EFB@mac.com> <7F49513D-1F3E-4965-89CA-581EDCB282D7@gmail.com> <5AD58156-2A06-4185-83D0-639FC75AAE84@gmail.com> Message-ID: <8D510BD7-64FC-4DFF-85F3-B658FEDCDB96@mac.com> Oops, yeah I forgot to add those to repository. They are in now so if you do an update then it should work. The GFF parser is something I just started working on. I think that I want to extend the BCAnnotation class to BCFeature, so that the parser returns a list of features. cheers Scott On Mar 5, 2011, at 11:22 AM, Koen van der Drift wrote: > Just for kicks, I downloaded the latest and greatest and tried to compile it. However, I get a missing file error BCParseGFF.h/.m - is this not yet added yet to the repository? > > Thanks, > > - Koen. > > > On Mar 1, 2011, at 2:31 PM, Scott Christley wrote: > >> Hello All, >> >> Here is some news about BioCocoa. >> >> * BioCocoa has now been packaged for the Debian (and Ubuntu) operating systems by the Debian-Med[1] team. This means that users can use the standard Debian packaging system to easily install a pre-built version of BioCocoa along with its dependencies (GNUstep mainly). It should make it in the next major release of Debian but is currently available in the "unstable" and "testing" distributions [2]. >> >> * There has been a number of new classes added to BioCocoa including BCParseOBO (reads ontology files in OBO format), BCBioPortalREST (download ontologies from the BioPortal web site), and a cluster of classes for reading compound, reaction and model databases for genome-scale metabolic models. The classes for metabolic models are being designed to interface with Argonne's SEED system [3]. >> >> * The BioSwarm framework has been added to BioCocoa SVN repository. BioSwarm is an OpenStep framework for computational biological modeling and simulation. It provides a suite of capabilities including gene network inference, flux-balance analysis for genome-scale metabolic models, classes for advanced spatial biological modeling, and GPU tools for running massively parallel simulations. BioSwarm includes much of the research that I've been doing for biological modeling, and I've made it public as I'm starting to gain a few users of the software. Plus I included it alongside BioCocoa because I think it is a complementary framework. >> >> * The BioCocoa wiki [4] has undergone some re-organization, check it out! >> >> cheers >> Scott >> >> [1] http://www.debian.org/devel/debian-med >> [2] http://packages.debian.org/search?keywords=libbiococoa >> [3] http://www.theseed.org/wiki/Main_Page >> [4] http://www.bioinformatics.org/biococoa/wiki/pmwiki.php >> >>>