From michael.watson at bbsrc.ac.uk Tue Sep 8 09:37:00 2009 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Tue, 8 Sep 2009 14:37:00 +0100 Subject: [BioSQL-l] Bioperl-db: provide password to Bio::DB::BioDB Message-ID: <8D08960C647E64438CE5740657CBBDC5010D2AC404@iahcexch1.iah.bbsrc.ac.uk> Hi Sorry if I am being a bit of a novice here, but can someone show me an example of providing a password to Bio::DB::BioDB->new? Thanks Mick From holland at eaglegenomics.com Tue Sep 8 13:37:29 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 8 Sep 2009 18:37:29 +0100 Subject: [BioSQL-l] Bioperl-db: provide password to Bio::DB::BioDB In-Reply-To: <8D08960C647E64438CE5740657CBBDC5010D2AC404@iahcexch1.iah.bbsrc.ac.uk> References: <8D08960C647E64438CE5740657CBBDC5010D2AC404@iahcexch1.iah.bbsrc.ac.uk> Message-ID: The parameters are the same as for Bio::DB::DBContextI: http://search.cpan.org/~cjfields/BioPerl-db-1.6.0/Bio/DB/DBContextI.pm cheers, Richard On 8 Sep 2009, at 14:37, michael watson (IAH-C) wrote: > Hi > > Sorry if I am being a bit of a novice here, but can someone show me > an example of providing a password to Bio::DB::BioDB->new? > > Thanks > Mick > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From ivan at biodec.com Tue Sep 15 08:48:28 2009 From: ivan at biodec.com (Ivan Rossi) Date: Tue, 15 Sep 2009 14:48:28 +0200 (CEST) Subject: [BioSQL-l] Announcing Plone4bio 1.0 Message-ID: -------------------------- Plone4bio 1.0 announcement -------------------------- BioDec is pleased to announce the new stable release of plone4bio. Plone4bio is a project to provide an integrated environment where it is possible to manage and analyze biological sequences within the Plone (http://plone.org) content management system. What's new ---------- In this release we have added a major feature, namely a product that let Plone act as a web interface to a BioSQL database. BioSQL (http://www.biosql.org/) is a generic relational model covering sequences, features, sequence and feature annotation, a reference taxonomy, and ontologies (or controlled vocabularies): a BioSQL database (as you know) can be used seamlessly from BioPerl, BioPython, BioJava, and BioRuby. A BioSQL databases is connected with a standard connection string to a plone4bio adapter, and then the content of the BioSQL database can be searched, using the Plone internal search engine and the plone collections, it can be browsed, including the usual graphical mapping of the features on the sequence, and in general handled by the standard Plone CMS machinery. Download and Project page ------------------------- The software is available at http://www.plone4bio.org The documentation is available at http://www.plone4bio.org/trac/wiki/Install The SVN repository is available at http://www.plone4bio.org/svn/ plone4bio mailing list: http://ackbar.biodec.com/cgi-bin/mailman/listinfo/p4b plone4bio demo site (read-only): http://p4bdemo.biodec.com Installation notes ------------------ The package to install to have a full plone4bio site running is plone4bio.buildout The plone4bio.base is just the package that defines a skeleton predictor: deriving from that it is possible to integrate any other application and visualize all the results together. biocomp.pscoils is an example predictor, encapsulating the pscoils algorithm by Fariselli et al. available at http://www.biocomp.unibo.it/ It is intended both as an example on how to integrate one's own predictor in the plone4bio framework and as a ready-to-use predictor for coiled-coils. Requirements: - python2.4 - python setup tools (Debian users: the python-setuptools package) - BioPython - PIL - BioPerl for some graphics Further information -------------------- Either the web site or the mailing list p4b at biodec.com For installation and documentation issues refer to README.txt and INSTALL.txt files from the archive or the script published on the plone4bio wiki site. plone4bio is published under the GPL. To contact BioDec S.r.l.: - Email: info at biodec.com - WWW: http://www.biodec.com - Phone: (+39)-051-0548263 - Fax: (+39)-051-7459582 -- Ivan Rossi, PhD - ivan AT biodec dot com OR ivan dot rossi3 AT unibo dot it BioDec Srl, Via Calzavecchio 20/2, I-40033 Casalecchio di Reno (BO), Italy Phone: (+39)-051-0548263 - Fax: (+39)-051-7459582 - http://www.biodec.com From jimp at compbio.dundee.ac.uk Thu Sep 24 06:22:30 2009 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Thu, 24 Sep 2009 11:22:30 +0100 Subject: [BioSQL-l] Announcing Plone4bio 1.0 In-Reply-To: References: Message-ID: <4ABB4866.9060200@compbio.dundee.ac.uk> Hi All. Ivan Rossi wrote: > BioDec is pleased to announce the new stable release of plone4bio. > > Plone4bio is a project to provide an integrated environment where it > is possible to manage and analyze biological sequences within the > Plone (http://plone.org) content management system. Has anyone had any luck with this ? I'm a novice when it comes to plone, and after a few hours of fiddling I still don't have a plone4bio site up and running... Jim. -- ------------------------------------------------------------------- J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From jimp at compbio.dundee.ac.uk Thu Sep 24 09:10:52 2009 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Thu, 24 Sep 2009 14:10:52 +0100 Subject: [BioSQL-l] Announcing Plone4bio 1.0 In-Reply-To: <4ABB4866.9060200@compbio.dundee.ac.uk> References: <4ABB4866.9060200@compbio.dundee.ac.uk> Message-ID: <4ABB6FDC.2020007@compbio.dundee.ac.uk> Hi again all. James Procter wrote: > Ivan Rossi wrote: >> BioDec is pleased to announce the new stable release of plone4bio. > Has anyone had any luck with this ? I'm a novice when it comes to plone, > and after a few hours of fiddling I still don't have a plone4bio site up > and running... after another half hour, I got a working plone4bio installation. If anyone is interested, let me know and I'll post a follow-up email regarding plone4bio's functionality w.r.t. browsing/querying biosql datasources. Jim. From biopython at maubp.freeserve.co.uk Thu Sep 24 16:25:58 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 24 Sep 2009 21:25:58 +0100 Subject: [BioSQL-l] Announcing Plone4bio 1.0 In-Reply-To: <4ABB6FDC.2020007@compbio.dundee.ac.uk> References: <4ABB4866.9060200@compbio.dundee.ac.uk> <4ABB6FDC.2020007@compbio.dundee.ac.uk> Message-ID: <320fb6e00909241325y1bb157cen6f075ba73252e968@mail.gmail.com> On Thu, Sep 24, 2009 at 2:10 PM, James Procter wrote: > > after another half hour, I got a working plone4bio installation. If anyone > is interested, let me know and I'll post a follow-up email regarding > plone4bio's functionality w.r.t. browsing/querying biosql datasources. That would be interesting, especially if you use multiple Bio* projects to load the database - this may indirectly show up areas where we need to be more inter-operable. Peter From michael.watson at bbsrc.ac.uk Fri Sep 25 04:13:00 2009 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Fri, 25 Sep 2009 09:13:00 +0100 Subject: [BioSQL-l] Announcing Plone4bio 1.0 In-Reply-To: <320fb6e00909241325y1bb157cen6f075ba73252e968@mail.gmail.com> References: <4ABB4866.9060200@compbio.dundee.ac.uk> <4ABB6FDC.2020007@compbio.dundee.ac.uk> <320fb6e00909241325y1bb157cen6f075ba73252e968@mail.gmail.com> Message-ID: <8D08960C647E64438CE5740657CBBDC5010D2AC5A2@iahcexch1.iah.bbsrc.ac.uk> Definitely interested in this! -----Original Message----- From: biosql-l-bounces at lists.open-bio.org [mailto:biosql-l-bounces at lists.open-bio.org] On Behalf Of Peter Sent: 24 September 2009 21:26 To: James Procter Cc: BioSQL-l at lists.open-bio.org Subject: Re: [BioSQL-l] Announcing Plone4bio 1.0 On Thu, Sep 24, 2009 at 2:10 PM, James Procter wrote: > > after another half hour, I got a working plone4bio installation. If anyone > is interested, let me know and I'll post a follow-up email regarding > plone4bio's functionality w.r.t. browsing/querying biosql datasources. That would be interesting, especially if you use multiple Bio* projects to load the database - this may indirectly show up areas where we need to be more inter-operable. Peter _______________________________________________ BioSQL-l mailing list BioSQL-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biosql-l From michael.watson at bbsrc.ac.uk Tue Sep 8 13:37:00 2009 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Tue, 8 Sep 2009 14:37:00 +0100 Subject: [BioSQL-l] Bioperl-db: provide password to Bio::DB::BioDB Message-ID: <8D08960C647E64438CE5740657CBBDC5010D2AC404@iahcexch1.iah.bbsrc.ac.uk> Hi Sorry if I am being a bit of a novice here, but can someone show me an example of providing a password to Bio::DB::BioDB->new? Thanks Mick From holland at eaglegenomics.com Tue Sep 8 17:37:29 2009 From: holland at eaglegenomics.com (Richard Holland) Date: Tue, 8 Sep 2009 18:37:29 +0100 Subject: [BioSQL-l] Bioperl-db: provide password to Bio::DB::BioDB In-Reply-To: <8D08960C647E64438CE5740657CBBDC5010D2AC404@iahcexch1.iah.bbsrc.ac.uk> References: <8D08960C647E64438CE5740657CBBDC5010D2AC404@iahcexch1.iah.bbsrc.ac.uk> Message-ID: The parameters are the same as for Bio::DB::DBContextI: http://search.cpan.org/~cjfields/BioPerl-db-1.6.0/Bio/DB/DBContextI.pm cheers, Richard On 8 Sep 2009, at 14:37, michael watson (IAH-C) wrote: > Hi > > Sorry if I am being a bit of a novice here, but can someone show me > an example of providing a password to Bio::DB::BioDB->new? > > Thanks > Mick > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From ivan at biodec.com Tue Sep 15 12:48:28 2009 From: ivan at biodec.com (Ivan Rossi) Date: Tue, 15 Sep 2009 14:48:28 +0200 (CEST) Subject: [BioSQL-l] Announcing Plone4bio 1.0 Message-ID: -------------------------- Plone4bio 1.0 announcement -------------------------- BioDec is pleased to announce the new stable release of plone4bio. Plone4bio is a project to provide an integrated environment where it is possible to manage and analyze biological sequences within the Plone (http://plone.org) content management system. What's new ---------- In this release we have added a major feature, namely a product that let Plone act as a web interface to a BioSQL database. BioSQL (http://www.biosql.org/) is a generic relational model covering sequences, features, sequence and feature annotation, a reference taxonomy, and ontologies (or controlled vocabularies): a BioSQL database (as you know) can be used seamlessly from BioPerl, BioPython, BioJava, and BioRuby. A BioSQL databases is connected with a standard connection string to a plone4bio adapter, and then the content of the BioSQL database can be searched, using the Plone internal search engine and the plone collections, it can be browsed, including the usual graphical mapping of the features on the sequence, and in general handled by the standard Plone CMS machinery. Download and Project page ------------------------- The software is available at http://www.plone4bio.org The documentation is available at http://www.plone4bio.org/trac/wiki/Install The SVN repository is available at http://www.plone4bio.org/svn/ plone4bio mailing list: http://ackbar.biodec.com/cgi-bin/mailman/listinfo/p4b plone4bio demo site (read-only): http://p4bdemo.biodec.com Installation notes ------------------ The package to install to have a full plone4bio site running is plone4bio.buildout The plone4bio.base is just the package that defines a skeleton predictor: deriving from that it is possible to integrate any other application and visualize all the results together. biocomp.pscoils is an example predictor, encapsulating the pscoils algorithm by Fariselli et al. available at http://www.biocomp.unibo.it/ It is intended both as an example on how to integrate one's own predictor in the plone4bio framework and as a ready-to-use predictor for coiled-coils. Requirements: - python2.4 - python setup tools (Debian users: the python-setuptools package) - BioPython - PIL - BioPerl for some graphics Further information -------------------- Either the web site or the mailing list p4b at biodec.com For installation and documentation issues refer to README.txt and INSTALL.txt files from the archive or the script published on the plone4bio wiki site. plone4bio is published under the GPL. To contact BioDec S.r.l.: - Email: info at biodec.com - WWW: http://www.biodec.com - Phone: (+39)-051-0548263 - Fax: (+39)-051-7459582 -- Ivan Rossi, PhD - ivan AT biodec dot com OR ivan dot rossi3 AT unibo dot it BioDec Srl, Via Calzavecchio 20/2, I-40033 Casalecchio di Reno (BO), Italy Phone: (+39)-051-0548263 - Fax: (+39)-051-7459582 - http://www.biodec.com From jimp at compbio.dundee.ac.uk Thu Sep 24 10:22:30 2009 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Thu, 24 Sep 2009 11:22:30 +0100 Subject: [BioSQL-l] Announcing Plone4bio 1.0 In-Reply-To: References: Message-ID: <4ABB4866.9060200@compbio.dundee.ac.uk> Hi All. Ivan Rossi wrote: > BioDec is pleased to announce the new stable release of plone4bio. > > Plone4bio is a project to provide an integrated environment where it > is possible to manage and analyze biological sequences within the > Plone (http://plone.org) content management system. Has anyone had any luck with this ? I'm a novice when it comes to plone, and after a few hours of fiddling I still don't have a plone4bio site up and running... Jim. -- ------------------------------------------------------------------- J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. From jimp at compbio.dundee.ac.uk Thu Sep 24 13:10:52 2009 From: jimp at compbio.dundee.ac.uk (James Procter) Date: Thu, 24 Sep 2009 14:10:52 +0100 Subject: [BioSQL-l] Announcing Plone4bio 1.0 In-Reply-To: <4ABB4866.9060200@compbio.dundee.ac.uk> References: <4ABB4866.9060200@compbio.dundee.ac.uk> Message-ID: <4ABB6FDC.2020007@compbio.dundee.ac.uk> Hi again all. James Procter wrote: > Ivan Rossi wrote: >> BioDec is pleased to announce the new stable release of plone4bio. > Has anyone had any luck with this ? I'm a novice when it comes to plone, > and after a few hours of fiddling I still don't have a plone4bio site up > and running... after another half hour, I got a working plone4bio installation. If anyone is interested, let me know and I'll post a follow-up email regarding plone4bio's functionality w.r.t. browsing/querying biosql datasources. Jim. From biopython at maubp.freeserve.co.uk Thu Sep 24 20:25:58 2009 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 24 Sep 2009 21:25:58 +0100 Subject: [BioSQL-l] Announcing Plone4bio 1.0 In-Reply-To: <4ABB6FDC.2020007@compbio.dundee.ac.uk> References: <4ABB4866.9060200@compbio.dundee.ac.uk> <4ABB6FDC.2020007@compbio.dundee.ac.uk> Message-ID: <320fb6e00909241325y1bb157cen6f075ba73252e968@mail.gmail.com> On Thu, Sep 24, 2009 at 2:10 PM, James Procter wrote: > > after another half hour, I got a working plone4bio installation. If anyone > is interested, let me know and I'll post a follow-up email regarding > plone4bio's functionality w.r.t. browsing/querying biosql datasources. That would be interesting, especially if you use multiple Bio* projects to load the database - this may indirectly show up areas where we need to be more inter-operable. Peter From michael.watson at bbsrc.ac.uk Fri Sep 25 08:13:00 2009 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Fri, 25 Sep 2009 09:13:00 +0100 Subject: [BioSQL-l] Announcing Plone4bio 1.0 In-Reply-To: <320fb6e00909241325y1bb157cen6f075ba73252e968@mail.gmail.com> References: <4ABB4866.9060200@compbio.dundee.ac.uk> <4ABB6FDC.2020007@compbio.dundee.ac.uk> <320fb6e00909241325y1bb157cen6f075ba73252e968@mail.gmail.com> Message-ID: <8D08960C647E64438CE5740657CBBDC5010D2AC5A2@iahcexch1.iah.bbsrc.ac.uk> Definitely interested in this! -----Original Message----- From: biosql-l-bounces at lists.open-bio.org [mailto:biosql-l-bounces at lists.open-bio.org] On Behalf Of Peter Sent: 24 September 2009 21:26 To: James Procter Cc: BioSQL-l at lists.open-bio.org Subject: Re: [BioSQL-l] Announcing Plone4bio 1.0 On Thu, Sep 24, 2009 at 2:10 PM, James Procter wrote: > > after another half hour, I got a working plone4bio installation. If anyone > is interested, let me know and I'll post a follow-up email regarding > plone4bio's functionality w.r.t. browsing/querying biosql datasources. That would be interesting, especially if you use multiple Bio* projects to load the database - this may indirectly show up areas where we need to be more inter-operable. Peter _______________________________________________ BioSQL-l mailing list BioSQL-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biosql-l