<div dir="ltr"><div>Hi Chris,</div><div><br></div><div>Thanks for the encouragement & suggestions. We will definitely cite the reference.</div><div><br></div><div>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.</div><div><br></div><div>weigang</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Mar 7, 2017 at 3:24 PM, Fields, Christopher J <span dir="ltr"><<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">Hi Weigang et al,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">Congrats on the manuscript! Apologies for the late reply, this one snuck by me.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">The FAQ (<a href="http://bioperl.org/FAQ.html)" target="_blank">http://bioperl.org/FAQ.html)</a> can answer some of these questions. In general I would refer to the citation (<a href="http://genome.cshlp.org/content/12/10/1611)" target="_blank">http://genome.cshlp.org/<wbr>content/12/10/1611)</a>;
if there is anyone in particular you wish to acknowledge they could be mentioned in that section.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">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).<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">chris<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><u></u> <u></u></span></p>
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<p class="MsoNormal"><b><span style="font-family:Calibri;color:black">From: </span>
</b><span style="font-family:Calibri;color:black">Bioperl-l <bioperl-l-bounces+cjfields=<a href="mailto:illinois.edu@mailman.open-bio.org" target="_blank">il<wbr>linois.edu@mailman.open-bio.<wbr>org</a>> on behalf of Weigang Qiu <<a href="mailto:weigangq@gmail.com" target="_blank">weigangq@gmail.com</a>><br>
<b>Date: </b>Monday, February 27, 2017 at 11:34 AM<br>
<b>To: </b>"<a href="mailto:bioperl-l@bioperl.org" target="_blank">bioperl-l@bioperl.org</a>" <<a href="mailto:bioperl-l@bioperl.org" target="_blank">bioperl-l@bioperl.org</a>><br>
<b>Cc: </b>Yozen Hernandez <<a href="mailto:yhernand@bu.edu" target="_blank">yhernand@bu.edu</a>>, Rocky Bernstein <<a href="mailto:rocky@cpan.org" target="_blank">rocky@cpan.org</a>><br>
<b>Subject: </b>[Bioperl-l] BpWrapper: acknowledgements & call for beta-testers<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas">Dear BopPerl developers & users,<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas">We are planning to formally release and write a manuscript on BbWrapper (</span><a href="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=" target="_blank"><span style="font-size:9.0pt;font-family:Consolas">https://github.com/bioperl/<wbr>p5-bpwrapper</span></a><span style="font-size:9.0pt;font-family:Consolas">),
currently including four command-line utilities (bioseq, bioaln, biotree, biopop) for manipulation of sequences, alignments, and phylogenetic trees.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas">We would like to ask for your input on the following two issues:<u></u><u></u></span></p>
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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?<u></u><u></u></li><li class="MsoNormal">
<span style="font-size:9.0pt;font-family:Consolas">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 <a href="http://bioperl.org" target="_blank">bioperl.org</a>, I have no idea how many (if any, besides
ourselves) have tried or used these wrapper scripts.</span><u></u><u></u></li></ul>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas">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.<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas">Thanks,<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="font-family:Consolas">weigang</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-family:Consolas">----------------</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-family:Consolas">Weigang Qiu, Ph.D. Associate Professor</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-family:Consolas">Department of Biological Sciences</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-family:Consolas">Hunter College of the City University of New York</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-family:Consolas">Belfer Research Building</span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-family:Consolas">Google Map: <a href="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" target="_blank">https://www.google.com/maps/<wbr>place/413+E+69th+St,+New+York,<wbr>+NY+10021/@40.7655886,-73.<wbr>9561743,17z/data=!3m1!4b1!4m2!<wbr>3m1!1s0x89c258c3d235f76f:<wbr>0x4f3d0d5d8a78fe6?hl=en</a></span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-family:Consolas">Lab Tel: <a href="tel:(212)%20896-0446" target="_blank" value="+12128960446">1-212-896-0446</a></span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-family:Consolas">Fax: <a href="tel:(212)%20772-5227" target="_blank" value="+12127725227">212-772-5227</a></span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-family:Consolas">Email: <a href="mailto:weigang@genectr.hunter.cuny.edu" target="_blank">weigang@genectr.hunter.cuny.<wbr>edu</a></span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-family:Consolas">Web:<a href="http://diverge.hunter.cuny.edu/labwiki/" target="_blank">http://diverge.hunter.<wbr>cuny.edu/labwiki/</a></span><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Consolas"><u></u> <u></u></span></p>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature" data-smartmail="gmail_signature">Weigang Qiu (邱伟刚)<br>117-14 Union Turnpike<br>AC3<br>Kew Gardens, New York 11415<br>1-917-678-3301</div>
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