[sib-courses] Small poll about an SIB Perl/BioPerl course

Gregoire Rossier gregoire.rossier at sib.swiss
Fri Apr 17 14:01:49 CEST 2020


Dear colleagues,


_Perl 5_ <https://www.perl.org/>is a well-established programming 
language still actively used and maintained, in particular in Life 
Sciences for which the _BioPerl_ <https://bioperl.org/>tools have been 
developed.

Examples of renowned bioinformatics resources using Perl are:

  *

    _Ensembl API_
    <https://m.ensembl.org/info/docs/api/index.html>/(BioPerl and
    regular Perl)/

  *

    _RepeatMasker_ <http://www.repeatmasker.org/>(Mask repeats in
    genomic sequences)

  *

    _Maker_ <http://www.yandell-lab.org/software/maker.html>(Genome
    Annotation and Curation) /(BioPerl and regular Perl)/

  *

    _Snippy_ <https://github.com/tseemann/snippy>(Rapid haploid variant
    calling and core genome alignment)

  *

    _primer3_ <https://github.com/primer3-org/primer3>(Select primers
    for polymerase chain reaction (PCR))

BioPerl usage example: 
_http://blogs.perl.org/users/zubenel/2020/03/comparing-coronavirus-sars-cov-2-spike-protein-sequences-with-bioperl.html_


SIB is considering to organize a Perl 5 course this year with a strong 
focus on Life Sciences applications. This 2-day course 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 the following poll 
<https://www.sib.swiss/form/view.php?id=63397>. The poll will close on 4 
May 2020.

Thank you for your time.

Best regards,

Grégoire

Grégoire Rossier

SIB Training Group, Vital-IT
SIB Swiss Institute of Bioinformatics
Quartier Sorge - Bâtiment Amphipôle
CH 1015 Lausanne - Switzerland

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