[Bioperl-l] BpWrapper: acknowledgements & call for beta-testers

Tue Mar 7 20:24:41 UTC 2017

Hi Weigang et al,

Congrats on the manuscript!  Apologies for the late reply, this one snuck by me.

The FAQ (http://bioperl.org/FAQ.html) can answer some of these questions.  In general I would refer to the citation (http://genome.cshlp.org/content/12/10/1611); if there is anyone in particular you wish to acknowledge they could be mentioned in that section.

I agree, having simpler front-end scripts/wrappers is a definite benefit long-term, primarily b/c you are creating a more user-friendly front-end.  I’m actually wondering where some of the more popular scripts in the core ‘scripts’ directory could be ported to this, it seems like a better long-term solution since these appear to be tested (one thing the scripts actually lack).

chris

From: Bioperl-l <bioperl-l-bounces+cjfields=illinois.edu at mailman.open-bio.org> on behalf of Weigang Qiu <weigangq at gmail.com>
Date: Monday, February 27, 2017 at 11:34 AM
To: "bioperl-l at bioperl.org" <bioperl-l at bioperl.org>
Cc: Yozen Hernandez <yhernand at bu.edu>, Rocky Bernstein <rocky at cpan.org>
Subject: [Bioperl-l] BpWrapper: acknowledgements & call for beta-testers

Dear BopPerl developers & users,

We are planning to formally release and write a manuscript on BbWrapper (https://github.com/bioperl/p5-bpwrapper<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bioperl_p5-2Dbpwrapper&d=DwMFAw&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=gIy3Q-j_l_SE6i2xe-Xz_MJoKSaejmd8ly8ocL33S2s&s=ysZ_nQMICzFIyF5MTqSiwGaVQ9AADfU_7f8WxoEswvo&e=>), currently including four command-line utilities (bioseq, bioaln, biotree, biopop) for manipulation of sequences, alignments, and phylogenetic trees.

We would like to ask for your input on the following two issues:

  *   How should we properly acknowledge the original developers (since most of the options are wrappers of BioPerl methods, not original codes by ourselves)? Is there an “official” statement of acknowledgement?
  *   I would like to invite you for beta-testing, commenting on, and contributing to BbWrapper. This is necessary, because, while we are honored to be hosted by bioperl.org, I have no idea how many (if any, besides ourselves) have tried  or used these wrapper scripts.
We believe the “Wrapper”-approach is more robust than many stand-alone sequence utilities out there because of this community of developers and users. Also, we believe these wrapper scripts could further popularize BioPerl among biologists by relieving them from writing object-oriented module callers.

Thanks,

weigang
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