From pedrolopes at ua.pt Sat Apr 7 11:30:49 2012 From: pedrolopes at ua.pt (Pedro Lopes) Date: Sat, 7 Apr 2012 16:30:49 +0100 Subject: [Open-bio-l] Abstract submission open for ISCBSC European Student Council Symposium Message-ID: <4C030C25292D4D749ECD30303F5EB77D@gmail.com> *** Apologies for multiple posting *** *** Please diffuse this call *** ISCB Student Council European Student Council Symposium 2012 The European Student Council Symposium aims at bringing together young computational biologists from all research areas and regions of the world. As the central part of our symposium, 8 student presentations will be selected from the submitted abstracts. This is your chance to present your work! We accept abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. All submitters are invited to bring a poster showcasing their work for inclusion in the F1000 repository. Travel Fellowships are available for everyone submitting to ESCS2012 and will be handled by ECCB12 organization. Awards will be given to best posters and presentations. Submission website: https://www.easychair.org/conferences/?conf=escs2012 Travel Fellowship information: http://escs.iscbsc.org/travel-fellowships General information: http://escs.iscbsc.org/ F1000 repository: http://f1000.com/ Important dates May 14: Abstract submission deadline June 25: Travel Fellowship submission deadline June 30: Abstract acceptance notification September 8: Student Symposium We look forward to receiving your abstract! Best regards, Pedro Lopes, Chair Florian Heer, Co-chair Pedro @pedrolopes (http://pedrolopes.net) | bioinformatics.ua.pt (http://bioinformatics.ua.pt) From francesco.strozzi at gmail.com Fri Apr 27 10:40:37 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Fri, 27 Apr 2012 16:40:37 +0200 Subject: [Open-bio-l] Bio::Faster update version 0.4.4 Message-ID: Hi all, I have updated the Bio::Faster gem for BioRuby. This gem allows for a fast parsing of FastQ files and it's based on a C extension. Many updates were done since the last version. The gem has been completely rewritten, both the C extension and the Ruby code. The C extension is now called through FFI, so this new gem works fine also with alternative Ruby interpreter, like JRuby. In particular, this new version can handle correctly the formatting errors that may be present in FastQ files, something that was not possible with the previous version due to the external C library used at the time. The RSpecs to build this new version were defined using the test files available from the official FastQ format paper (http://nar.oxfordjournals.org/content/38/6/1767.abstract). The code is available here: https://github.com/fstrozzi/bioruby-faster The new version of the gem is available on RubyGems: gem install bio-faster If you have the chance, please check this new version at let me know of any bugs or problems you may find. Please note that since version 0.4.0 bio-faster does not support parsing FastA files anymore. The code is now only focused on FastQ format. Cheers -- Francesco From pjotr.public41 at thebird.nl Fri Apr 27 15:54:56 2012 From: pjotr.public41 at thebird.nl (Pjotr Prins) Date: Fri, 27 Apr 2012 21:54:56 +0200 Subject: [Open-bio-l] Bio::Faster update version 0.4.4 In-Reply-To: References: Message-ID: <20120427195456.GA14022@thebird.nl> Brilliant. If I see this correctly, Francesco has also written a new C parser, pretty much overnight. Pj. On Fri, Apr 27, 2012 at 04:40:37PM +0200, Francesco Strozzi wrote: > Hi all, > I have updated the Bio::Faster gem for BioRuby. This gem allows for a > fast parsing of FastQ files and it's based on a C extension. > Many updates were done since the last version. The gem has been > completely rewritten, both the C extension and the Ruby code. The C > extension is now called through FFI, so this new gem works fine also > with alternative Ruby interpreter, like JRuby. > In particular, this new version can handle correctly the formatting > errors that may be present in FastQ files, something that was not > possible with the previous version due to the external C library used > at the time. > The RSpecs to build this new version were defined using the test files > available from the official FastQ format paper > (http://nar.oxfordjournals.org/content/38/6/1767.abstract). > > The code is available here: https://github.com/fstrozzi/bioruby-faster > The new version of the gem is available on RubyGems: gem install bio-faster > > If you have the chance, please check this new version at let me know > of any bugs or problems you may find. > > Please note that since version 0.4.0 bio-faster does not support > parsing FastA files anymore. The code is now only focused on FastQ > format. > > Cheers > > -- > > Francesco > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l > From pedrolopes at ua.pt Sat Apr 7 15:30:49 2012 From: pedrolopes at ua.pt (Pedro Lopes) Date: Sat, 7 Apr 2012 16:30:49 +0100 Subject: [Open-bio-l] Abstract submission open for ISCBSC European Student Council Symposium Message-ID: <4C030C25292D4D749ECD30303F5EB77D@gmail.com> *** Apologies for multiple posting *** *** Please diffuse this call *** ISCB Student Council European Student Council Symposium 2012 The European Student Council Symposium aims at bringing together young computational biologists from all research areas and regions of the world. As the central part of our symposium, 8 student presentations will be selected from the submitted abstracts. This is your chance to present your work! We accept abstracts covering both scientific studies as well as novel tools and applications in the field of computational biology and bioinformatics. All submitters are invited to bring a poster showcasing their work for inclusion in the F1000 repository. Travel Fellowships are available for everyone submitting to ESCS2012 and will be handled by ECCB12 organization. Awards will be given to best posters and presentations. Submission website: https://www.easychair.org/conferences/?conf=escs2012 Travel Fellowship information: http://escs.iscbsc.org/travel-fellowships General information: http://escs.iscbsc.org/ F1000 repository: http://f1000.com/ Important dates May 14: Abstract submission deadline June 25: Travel Fellowship submission deadline June 30: Abstract acceptance notification September 8: Student Symposium We look forward to receiving your abstract! Best regards, Pedro Lopes, Chair Florian Heer, Co-chair Pedro @pedrolopes (http://pedrolopes.net) | bioinformatics.ua.pt (http://bioinformatics.ua.pt) From francesco.strozzi at gmail.com Fri Apr 27 14:40:37 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Fri, 27 Apr 2012 16:40:37 +0200 Subject: [Open-bio-l] Bio::Faster update version 0.4.4 Message-ID: Hi all, I have updated the Bio::Faster gem for BioRuby. This gem allows for a fast parsing of FastQ files and it's based on a C extension. Many updates were done since the last version. The gem has been completely rewritten, both the C extension and the Ruby code. The C extension is now called through FFI, so this new gem works fine also with alternative Ruby interpreter, like JRuby. In particular, this new version can handle correctly the formatting errors that may be present in FastQ files, something that was not possible with the previous version due to the external C library used at the time. The RSpecs to build this new version were defined using the test files available from the official FastQ format paper (http://nar.oxfordjournals.org/content/38/6/1767.abstract). The code is available here: https://github.com/fstrozzi/bioruby-faster The new version of the gem is available on RubyGems: gem install bio-faster If you have the chance, please check this new version at let me know of any bugs or problems you may find. Please note that since version 0.4.0 bio-faster does not support parsing FastA files anymore. The code is now only focused on FastQ format. Cheers -- Francesco From pjotr.public41 at thebird.nl Fri Apr 27 19:54:56 2012 From: pjotr.public41 at thebird.nl (Pjotr Prins) Date: Fri, 27 Apr 2012 21:54:56 +0200 Subject: [Open-bio-l] Bio::Faster update version 0.4.4 In-Reply-To: References: Message-ID: <20120427195456.GA14022@thebird.nl> Brilliant. If I see this correctly, Francesco has also written a new C parser, pretty much overnight. Pj. On Fri, Apr 27, 2012 at 04:40:37PM +0200, Francesco Strozzi wrote: > Hi all, > I have updated the Bio::Faster gem for BioRuby. This gem allows for a > fast parsing of FastQ files and it's based on a C extension. > Many updates were done since the last version. The gem has been > completely rewritten, both the C extension and the Ruby code. The C > extension is now called through FFI, so this new gem works fine also > with alternative Ruby interpreter, like JRuby. > In particular, this new version can handle correctly the formatting > errors that may be present in FastQ files, something that was not > possible with the previous version due to the external C library used > at the time. > The RSpecs to build this new version were defined using the test files > available from the official FastQ format paper > (http://nar.oxfordjournals.org/content/38/6/1767.abstract). > > The code is available here: https://github.com/fstrozzi/bioruby-faster > The new version of the gem is available on RubyGems: gem install bio-faster > > If you have the chance, please check this new version at let me know > of any bugs or problems you may find. > > Please note that since version 0.4.0 bio-faster does not support > parsing FastA files anymore. The code is now only focused on FastQ > format. > > Cheers > > -- > > Francesco > _______________________________________________ > Open-Bio-l mailing list > Open-Bio-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/open-bio-l >