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<div class="moz-text-html" lang="x-unicode"><font face="Helvetica,
Arial, sans-serif"><span style="font-size: 11pt; color: rgb(0,
0, 0);">Dear colleagues,</span></font></div>
<div class="moz-text-html" lang="x-unicode"><font face="Helvetica,
Arial, sans-serif"><span style="font-size: 11pt; color: rgb(0,
0, 0);"><br>
</span></font></div>
<div class="moz-text-html" lang="x-unicode"><font face="Helvetica,
Arial, sans-serif"><span style="font-size: 11pt; color: rgb(0,
0, 0);"><br>
</span></font> <font face="Helvetica, Arial, sans-serif"> </font>
<p
style="margin-top:0pt;margin-bottom:10pt;border:none;mso-border-left-alt:none;mso-border-top-alt:none;mso-border-right-alt:none;mso-border-bottom-alt:none;mso-border-between:none"><font
face="Helvetica, Arial, sans-serif"><a
href="https://www.perl.org/" title=""><span
style="font-size: 11pt; color: rgb(5, 99, 193);"><u>Perl 5</u></span></a><span
style="font-size: 11pt; color: rgb(0, 0, 0);"> is </span><span
style="font-size: 11pt; color: rgb(0, 0, 0);">a
well-established programming language still actively used
and maintained, in particular in Life Sciences for which the
</span><a href="https://bioperl.org/" title=""><span
style="font-size: 11pt; color: rgb(5, 99, 193);"><u>BioPerl</u></span></a><span
style="font-size: 11pt; color: rgb(0, 0, 0);"> tools have
been developed.</span></font></p>
<font face="Helvetica, Arial, sans-serif"> </font>
<p
style="margin-top:0pt;margin-bottom:10pt;border:none;mso-border-left-alt:none;mso-border-top-alt:none;mso-border-right-alt:none;mso-border-bottom-alt:none;mso-border-between:none"><font
face="Helvetica, Arial, sans-serif"> </font></p>
<font face="Helvetica, Arial, sans-serif"> </font>
<p
style="margin-top:0pt;margin-bottom:10pt;border:none;mso-border-left-alt:none;mso-border-top-alt:none;mso-border-right-alt:none;mso-border-bottom-alt:none;mso-border-between:none"><font
face="Helvetica, Arial, sans-serif"><span style="font-size:
11pt; color: rgb(0, 0, 0);">Examples of renowned
bioinformatics resources using Perl are:</span></font></p>
<font face="Helvetica, Arial, sans-serif"> </font>
<ul style="padding-left:40px">
<li style="list-style-type: disc">
<p
style="margin-left:35.45pt;text-indent:-18pt;margin-top:0pt;margin-bottom:10pt;border:none;mso-border-left-alt:none;mso-border-top-alt:none;mso-border-right-alt:none;mso-border-bottom-alt:none;mso-border-between:none"><font
face="Helvetica, Arial, sans-serif"><a
href="https://m.ensembl.org/info/docs/api/index.html"
title=""><span style="font-size: 11pt; color: rgb(5, 99,
193);"><u>Ensembl API</u></span></a><span
style="font-size: 11pt; color: rgb(0, 0, 0);"> </span><span
style="font-size: 11pt; color: rgb(0, 0, 0);"><i>(BioPerl
and regular Perl)</i></span></font></p>
</li>
<li style="list-style-type: disc">
<p
style="margin-left:35.45pt;text-indent:-18pt;margin-top:0pt;margin-bottom:10pt;border:none;mso-border-left-alt:none;mso-border-top-alt:none;mso-border-right-alt:none;mso-border-bottom-alt:none;mso-border-between:none"><font
face="Helvetica, Arial, sans-serif"><a
href="http://www.repeatmasker.org/" title=""><span
style="font-size: 11pt; color: rgb(5, 99, 193);"><u>RepeatMasker</u></span></a><span
style="font-size: 11pt; color: rgb(0, 0, 0);"> (Mask
repeats in genomic sequences)</span></font></p>
</li>
<li style="list-style-type: disc">
<p
style="margin-left:35.45pt;text-indent:-18pt;margin-top:0pt;margin-bottom:10pt;border:none;mso-border-left-alt:none;mso-border-top-alt:none;mso-border-right-alt:none;mso-border-bottom-alt:none;mso-border-between:none"><font
face="Helvetica, Arial, sans-serif"><a
href="http://www.yandell-lab.org/software/maker.html"
title=""><span style="font-size: 11pt; color: rgb(5, 99,
193);"><u>Maker</u></span></a><span style="font-size:
11pt; color: rgb(0, 0, 0);"> (</span><span
style="font-size: 11pt; color: rgb(0, 0, 0);">Genome
Annotation and Curation</span><span style="font-size:
11pt; color: rgb(0, 0, 0);">) </span><span
style="font-size: 11pt; color: rgb(0, 0, 0);"><i>(BioPerl
and regular Perl)</i></span></font></p>
</li>
<li style="list-style-type: disc">
<p
style="margin-left:35.45pt;text-indent:-18pt;margin-top:0pt;margin-bottom:10pt;border:none;mso-border-left-alt:none;mso-border-top-alt:none;mso-border-right-alt:none;mso-border-bottom-alt:none;mso-border-between:none"><font
face="Helvetica, Arial, sans-serif"><a
href="https://github.com/tseemann/snippy" title=""><span
style="font-size: 11pt; color: rgb(5, 99, 193);"><u>Snippy</u></span></a><span
style="font-size: 11pt; color: rgb(0, 0, 0);"> (</span><span
style="font-size: 11pt; color: rgb(0, 0, 0);">Rapid
haploid variant calling and core genome alignment)</span></font></p>
</li>
<li style="list-style-type: disc">
<p
style="margin-left:35.45pt;text-indent:-18pt;margin-top:0pt;margin-bottom:10pt;border:none;mso-border-left-alt:none;mso-border-top-alt:none;mso-border-right-alt:none;mso-border-bottom-alt:none;mso-border-between:none"><font
face="Helvetica, Arial, sans-serif"><a
href="https://github.com/primer3-org/primer3" title=""><span
style="font-size: 11pt; color: rgb(5, 99, 193);"><u>primer3</u></span></a><span
style="font-size: 11pt; color: rgb(0, 0, 0);"> </span><span
style="font-size: 11pt; color: rgb(0, 0, 0);">(</span><span
style="font-size: 11pt; color: rgb(0, 0, 0);">S</span><span
style="font-size: 11pt; color: rgb(0, 0, 0);">elect
primers for polymerase chain reaction (PCR)</span><span
style="font-size: 11pt; color: rgb(0, 0, 0);">)</span></font></p>
</li>
</ul>
<font face="Helvetica, Arial, sans-serif"> </font>
<p
style="margin-left:35.45pt;margin-top:0pt;margin-bottom:10pt;border:none;mso-border-left-alt:none;mso-border-top-alt:none;mso-border-right-alt:none;mso-border-bottom-alt:none;mso-border-between:none"><font
face="Helvetica, Arial, sans-serif"><span style="font-size:
11pt; color: rgb(0, 0, 0);">BioPerl usage example: </span><a
href="http://blogs.perl.org/users/zubenel/2020/03/comparing-coronavirus-sars-cov-2-spike-protein-sequences-with-bioperl.html"
title=""><span style="font-size: 11pt; color: rgb(5, 99,
193);"><u>http://blogs.perl.org/users/zubenel/2020/03/comparing-coronavirus-sars-cov-2-spike-protein-sequences-with-bioperl.html</u></span></a></font></p>
<font face="Helvetica, Arial, sans-serif"> </font>
<p><font face="Helvetica, Arial, sans-serif"><br>
</font></p>
<p><font face="Helvetica, Arial, sans-serif">SIB is considering to
organize <span style="font-size: 11pt; color: rgb(0, 0, 0);">a
Perl 5 course this year with a strong focus on Life Sciences
applications. This 2-day course </span><span
style="font-size: 11pt; color: rgb(0, 0, 0);"><span
style="font-size: 11pt; color: rgb(0, 0, 0);">would
include an introduction to Perl, an introduction to
regular expressions (RegEx) and a few example of life
science use cases using Perl/BioPerl. To this end, we
would like to evaluate the community interest with <a
href="https://www.sib.swiss/form/view.php?id=63397">the
following poll</a>. The poll will close on 4 May 2020.</span></span></font></p>
<p><font face="Helvetica, Arial, sans-serif"><span
style="font-size: 11pt; color: rgb(0, 0, 0);"><span
style="font-size: 11pt; color: rgb(0, 0, 0);">Thank you
for your time.</span></span></font></p>
<p><font face="Helvetica, Arial, sans-serif">Best regards,</font></p>
Grégoire<br>
<p><span
style="font-family:'Arial';font-size:11pt;color:#000000;mso-style-textfill-fill-color:#000000"></span></p>
<div class="moz-signature">
<p style="font-size:12px;color:#585858">Grégoire Rossier<br>
<br>
SIB Training Group, Vital-IT<br>
SIB Swiss Institute of Bioinformatics<br>
Quartier Sorge - Bâtiment Amphipôle<br>
CH 1015 Lausanne - Switzerland<br>
<br>
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