How to cite Perl Dancer
Hi All, while we've built a little bioinformatics application based on Dancer (http://rna.tbi.univie.ac.at/TSSAR) and are currently writing a paper about it, I was wondering how to correctly cite the Perl Dancer project. Is there any official manuscript around apart from the Dancer website? Best, Michael
On 10/06/2013 14:16, Michael Wolfinger wrote:
Hi All, while we've built a little bioinformatics application based on Dancer (http://rna.tbi.univie.ac.at/TSSAR) and are currently writing a paper about it, I was wondering how to correctly cite the Perl Dancer project. Is there any official manuscript around apart from the Dancer website?
I can't answer that for you sorry, but I am interested in your web-site. I'm also using D2 to build a NGS web application (though it will be on a 'private' intranet). I'm interested in why you use a Perl web framework but Java for the main data processing engine, not Perl and the BioPerl library. Not fast enough maybe? Java has better Seq libraries? Or have I misunderstood the documentation and Java is just used for the the client-side pre-processing? -- Richard Jones
You're right. Our Java client is just used for pre-processing the raw NGS data, extracting read start information from mapped NGS data (since we do not want users to upload gigabyte-sized BAM/SAM files). We are using Dancer as lightweight interface between the client and the effective (Perl and R-based) statistics tools, ie. our Dancer application controls calculation statistics and post-processing jobs submitted to the grid engine cluster and does the session handling and backend stuff. It the tool gets adopted by the scientific community, we will publish a RESTful API for our transcription start site annotation web service. Michael On 10.06.13 15:54, Richard Jones wrote:
On 10/06/2013 14:16, Michael Wolfinger wrote:
Hi All, while we've built a little bioinformatics application based on Dancer (http://rna.tbi.univie.ac.at/TSSAR) and are currently writing a paper about it, I was wondering how to correctly cite the Perl Dancer project. Is there any official manuscript around apart from the Dancer website?
I can't answer that for you sorry, but I am interested in your web-site. I'm also using D2 to build a NGS web application (though it will be on a 'private' intranet). I'm interested in why you use a Perl web framework but Java for the main data processing engine, not Perl and the BioPerl library. Not fast enough maybe? Java has better Seq libraries? Or have I misunderstood the documentation and Java is just used for the the client-side pre-processing?
-- Dr. Michael Thomas Wolfinger SFB RNA-REG consortium - Bioinformatics University of Vienna CIBIV, Dr. Bohr-Gasse 9, 1030 Vienna, Austria [p] +43 1 4277 24027 TBI, Währingerstrasse 17, 1090 Vienna, Austria [p] +43 1 4277 52747 [m] michael.wolfinger@univie.ac.at [w] www.tbi.univie.ac.at/~mtw
On 10/06/2013 15:55, Michael Wolfinger wrote:
we do not want users to upload gigabyte-sized BAM/SAM files). We are using Dancer as lightweight interface between the client and the effective (Perl and R-based) statistics tools,
OK, thanks for the clarification. Is your stats tool publicly available? Does it use Statistics::R or some other Perl/R interface? -- Richard Jones
Here is the link to the stand-alone version of TSSAR (just statistics, no post-processing or Dancer code) http://rna.tbi.univie.ac.at/TSSAR/download/TSSAR_0.6.zip Best, Michael On 10.06.13 17:11, Richard Jones wrote:
On 10/06/2013 15:55, Michael Wolfinger wrote:
we do not want users to upload gigabyte-sized BAM/SAM files). We are using Dancer as lightweight interface between the client and the effective (Perl and R-based) statistics tools,
OK, thanks for the clarification. Is your stats tool publicly available? Does it use Statistics::R or some other Perl/R interface?
On Mon, Jun 10, 2013 at 9:16 AM, Michael Wolfinger <michael.wolfinger@univie.ac.at> wrote:
Hi All, while we've built a little bioinformatics application based on Dancer (http://rna.tbi.univie.ac.at/TSSAR) and are currently writing a paper about it, I was wondering how to correctly cite the Perl Dancer project. Is there any official manuscript around apart from the Dancer website?
I think the Perl Dancer website is probably the most useful academic citation. David -- David Golden <xdg@xdg.me> Take back your inbox! → http://www.bunchmail.com/ Twitter/IRC: @xdg
participants (3)
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David Golden -
Michael Wolfinger -
Richard Jones