<html><head></head><body><div style="color:#000; background-color:#fff; font-family:Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10px"><div id="yui_3_16_0_1_1496997591588_52164" dir="ltr"><span id="yui_3_16_0_1_1496997591588_52201">I would be in favor of removing Bio.NeuralNetwork. It was useful in the past, but nowadays it seems out of scope for Biopython, and if scikit-learn offers a better solution then we don't need this module in Biopython.</span></div><div id="yui_3_16_0_1_1496997591588_52244" dir="ltr"><br><span id="yui_3_16_0_1_1496997591588_52201"></span></div><div dir="ltr"><span id="yui_3_16_0_1_1496997591588_52201">Best,</span></div><div dir="ltr"><span id="yui_3_16_0_1_1496997591588_52201">-Michiel</span></div> <div class="qtdSeparateBR"><br><br></div><div style="display: block;" class="yahoo_quoted"> <div style="font-family: Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 10px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"><font face="Arial" size="2"> On Thursday, June 8, 2017 1:36 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:<br></font></div> <br><br> <div class="y_msg_container"><div dir="ltr">Hi Adil,<br clear="none"><br clear="none">So you'd be in favour of us deprecating and later removing<br clear="none">Bio.NeuralNetwork which the original author Brad suggested<br clear="none">on the other thread?<br clear="none"><br clear="none"><a shape="rect" href="http://mailman.open-bio.org/pipermail/biopython-dev/2017-June/021719.html" target="_blank">http://mailman.open-bio.org/pipermail/biopython-dev/2017-June/021719.html</a><br clear="none"><br clear="none">Regards,<br clear="none"><br clear="none">Peter<br clear="none"><br clear="none">On Wed, Jun 7, 2017 at 5:18 PM, Adil Iqbal <<a shape="rect" ymailto="mailto:aiqbal85@gmail.com" href="mailto:aiqbal85@gmail.com">aiqbal85@gmail.com</a>> wrote:<br clear="none">> Hey guys,<br clear="none">><br clear="none">> I wanted to try and save the machine learning module somehow, but based on<br clear="none">> the varied applications of machine learning in bioinformatics, really the<br clear="none">> best package to use is scikit-learn. It covers everything from Bayesian<br clear="none">> networks, hierarchical clustering, decision trees, etc.<br clear="none">><br clear="none">> I suppose biopython could offer pre-built, easily modified networks for the<br clear="none">> most common use-cases, that is, protein folding and gene pattern<br clear="none">> recognition. Though we would need to use scikit-learn (or other machine<br clear="none">> learning package) as a dependency.<br clear="none">><br clear="none">> Another option would be to scrap the machine learning suite and focus more<br clear="none">> on data management.<br clear="none">><br clear="none">> Best,<br clear="none">> Adil<br clear="none">><br clear="none">> _______________________________________________<br clear="none">> Biopython-dev mailing list<br clear="none">> <a shape="rect" ymailto="mailto:Biopython-dev@mailman.open-bio.org" href="mailto:Biopython-dev@mailman.open-bio.org">Biopython-dev@mailman.open-bio.org</a><br clear="none">> <a shape="rect" href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython-dev</a><div class="yqt6052674167" id="yqtfd50247"><br clear="none">_______________________________________________<br clear="none">Biopython-dev mailing list<br clear="none"><a shape="rect" ymailto="mailto:Biopython-dev@mailman.open-bio.org" href="mailto:Biopython-dev@mailman.open-bio.org">Biopython-dev@mailman.open-bio.org</a><br clear="none"><a shape="rect" href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython-dev</a><br clear="none"></div></div><br><br></div> </div> </div> </div></div></body></html>