BioPerl

Last year's Google Summer of Code 2014 was very productive for the OBF with six students working on Bio* and related bioinformatics projects. We applied to be part of GSoC 2015, but unfortunately this year were not accepted. Continue reading →

Last year's Google Summer of Code 2014 was very productive for the OBF with six students working on Bio* and related bioinformatics projects. We applied to be part of GSoC 2015, but unfortunately this year were not accepted. Continue reading →

Congrats Demian! chris On Jan 13, 2015, at 8:52 AM, Demian Riccardi <demianriccardi< at >gmail.com<mailto:demianriccardi< at >gmail.com>> wrote: Hello BioPerl community! HackaMol<https://metacpan.org/pod/HackaMol> ... [More] 0.01 has been released. The library, very much inspired by BioPerl, targets structural analysis and multiscale molecular modeling. While this is an early release, I've pushed it as far as I could over the past year. There are surely areas that need work. Contributions are welcome! Fork me on Github!<https://github.com/demianriccardi/HackaMol> Demian _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org<mailto:Bioperl-l< at >mailman.open-bio.org> http://mailman.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l [Less]

Hello! Not too familiar w/ Bioperl and want to make sure i've properly installed on my VM ubuntu 14.4 server w/ git. http://www.bioperl.org/wiki/BioPerl_Dependencies http://www.bioperl.org/wiki/Using_Git sudo apt-get update sudo apt-get upgrade sudo ... [More] apt-get check sudo apt-get autoclean sudo apt-get install build-essential git gcc sudo apt-get install libexpat1 expat sudo apt-get install libgd-dev (unable to locate libgd recommended on gmod.org/wiki/BioPerl Dependencies Outside perl) sudo apt-get install libssl-dev sudo apt-get install libpq-dev sudo apt-get install libdb-dev libperl-dev sudo apt-get install libgd-gd2-perl sudo apt-get install libxml2 sudo apt-get install libxml2-dev Installed local::lib manually for perl modules. Set environment path echo '[ $SHLVL -eq 1 ] && eval "$(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib)"' >>~/.bashrc cpan> install Bundle::CPAN (archive::zip failed? pff!) cpan> install Bundle::BioPerl Failed during this command: LDS/AcePerl-1.92.tar.gz : make_ [Less]

Hello BioPerl community! HackaMol <https://metacpan.org/pod/HackaMol> 0.01 has been released. The library, very much inspired by BioPerl, targets structural analysis and multiscale molecular modeling. While this is an early release, I've ... [More] pushed it as far as I could over the past year. There are surely areas that need work. Contributions are welcome! Fork me on Github! <https://github.com/demianriccardi/HackaMol> Demian _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l [Less]

I will likely start working on a new BioPerl release in the next week or two to attempt fixing some of the CPAN indexing problems that have plagued us in the last few releases (final version to be mentioned when that is fixed :). Along those ... [More] lines, a few things when committing code: 1) Add yourself to the AUTHORS file if you have ben making code changes. We like to give credit where credit is due! 2) Please make sure to update the ‘Changes’ file if appropriate. This is particularly important if the changes are addressing bugs or adding functionality. 3) Make sure anything potentially code-breaking is made on a branch first and merged in. This hasn’t been a problem recently (the coveralls work that Franscisco is unfortunately easier to deal with on master, so that is a clear exception). Thanks! chris [Less]

Our company is beefing up our overall computer security. This includes making modifications to many custom legacy web based Perl cgi bioinformatics databases, as well as refactoring a few of these applications using the Perl Catalyst framework. We ... [More] are looking for a consultant with expertise in Perl web security, preferably someone who also has experience with Catalyst best practices to review our code and make recommendations and/or rewrite some necessary pieces. If they possess any relevant web application security credentials, that would be a plus. Thanks in advance for any help you can provide in our search. -- Doug Hershberger _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l [Less]

Hi Chris, thanks for you response! No, there hasn't been a response yet. The solution with add_tag_value('Parent') works for me tough. Best, Daniel On 28.09.2014 05:26, Fields, Christopher J wrote: >

Hi All, I tried to use PAML:Yn00 to run yn00 and parse the result. However, no results were given. Does anyone know what might be the problem? The following code is obtained from ... [More] http://search.cpan.org/dist/BioPerl-Run/lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm use Bio::Tools::Run::Phylo::PAML::Yn00; use Bio::AlignIO; my $alignio = Bio::AlignIO->new( -format => 'fasta', -file => "$ARGV[0]" ); my $aln = $alignio->next_aln; my $yn = Bio::Tools::Run::Phylo::PAML::Yn00->new(); $yn->alignment($aln); my ( $rc, $parser ) = $yn->run; while ( my $result = $parser->next_result ) { my < at >otus = $result->get_seqs(); my $MLmatrix = $result->get_MLmatrix(); #0 and 1 correspond to the 1st and 2nd entry in the < at >otus array my $dN = $MLmatrix->[0]->[1]->{dN}; my $dS = $MLmatrix->[0]->[1]->{dS}; my $kaks = $MLmatrix->[0]->[1]->{omega}; print "Ka = $dN Ks = $dS Ka/Ks = $kaks\n"; } ########################################################### Alignment: aaattgttgttg aacaatttgttg Yours [Less]

Greetings Everyone, On behalf of a number of software developers, end-users, publishers associated with the scientific analysis community, we would like to invite all of you to review a document generated as a result of a NIH BD2K supported ... [More] meeting that focused on the opportunities and challenges of developing a software management ecosystem that could be valuable for finding and linking software, publications and users in the research community. You may be also be aware of a related project, the Data Discovery Index, which will be fully integrated with the software system. The product of this workshop and the subsequent discussion is a document which details the opportunities and challenges of developing a Software Discovery Index that would enable researchers to find, cite, and link software and analysis tools publications and researchers. To ensure that the opportunities, challenges, and recommendations detailed in the document reflect the breadth of experience from the community, we are seeking your [Less]