Re: BpWrapper: acknowledgements & call for beta-testers

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Re: BpWrapper: acknowledgements & call for beta-testers

Fields, Christopher J

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=[hidden email]> on behalf of Weigang Qiu <[hidden email]>
Date: Monday, February 27, 2017 at 11:34 AM
To: "[hidden email]" <[hidden email]>
Cc: Yozen Hernandez <[hidden email]>, Rocky Bernstein <[hidden email]>
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), 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

----------------

Weigang Qiu, Ph.D. Associate Professor

Department of Biological Sciences

Hunter College of the City University of New York

Belfer Research Building

413 East 69th Street, Room 402

New York, NY 10021

Google Map: https://www.google.com/maps/place/413+E+69th+St,+New+York,+NY+10021/@40.7655886,-73.9561743,17z/data=!3m1!4b1!4m2!3m1!1s0x89c258c3d235f76f:0x4f3d0d5d8a78fe6?hl=en

Office Tel: 1-212-896-0445

Lab Tel: 1-212-896-0446

Fax: 212-772-5227

Web:http://diverge.hunter.cuny.edu/labwiki/

 


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Re: BpWrapper: acknowledgements & call for beta-testers

Weigang Qiu-2
Hi Chris,

Thanks for the encouragement & suggestions. We will definitely cite the reference.

Rocky developed formal testing scripts on multiple OS & versions of the same OS. We will take a look at the scripts and see what could popular one be wrapped.

weigang

On Tue, Mar 7, 2017 at 3:24 PM, Fields, Christopher J <[hidden email]> wrote:

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=[hidden email]> on behalf of Weigang Qiu <[hidden email]>
Date: Monday, February 27, 2017 at 11:34 AM
To: "[hidden email]" <[hidden email]>
Cc: Yozen Hernandez <[hidden email]>, Rocky Bernstein <[hidden email]>
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), 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

----------------

Weigang Qiu, Ph.D. Associate Professor

Department of Biological Sciences

Hunter College of the City University of New York

Belfer Research Building

413 East 69th Street, Room 402

New York, NY 10021

Office Tel: <a href="tel:(212)%20896-0445" target="_blank" value="+12128960445">1-212-896-0445

Lab Tel: <a href="tel:(212)%20896-0446" target="_blank" value="+12128960446">1-212-896-0446

Fax: <a href="tel:(212)%20772-5227" target="_blank" value="+12127725227">212-772-5227

 




--
Weigang Qiu (邱伟刚)
117-14 Union Turnpike
AC3
Kew Gardens, New York 11415
1-917-678-3301

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