Question: Beginners resources for biologists to learn Perl applications
5
gravatar for Ram Sharma
8.0 years ago by
Ram Sharma50
Ram Sharma50 wrote:

I want to start to learn perl and bioperl. Can somebody list useful online resources?

education bioperl perl • 3.6k views
ADD COMMENTlink modified 5.1 years ago by Obi Griffith18k • written 8.0 years ago by Ram Sharma50
2

http://www.bioperl.org/wiki/HOWTO:Beginners would seem the obvious starting point.

ADD REPLYlink modified 5 months ago by RamRS25k • written 8.0 years ago by Neilfws48k
5
gravatar for SES
8.0 years ago by
SES8.3k
Vancouver, BC
SES8.3k wrote:

Have a look at this excellent introduction to Unix and Perl from Ian Korf's lab: http://korflab.ucdavis.edu/Unix_and_Perl/

For BioPerl specifically, you'll want to take a look at the HOWTOs on the BioPerl wiki to see some worked examples.

The Beginning Perl for Bioinformatics by Tisdall is probably a must-have for biologists wanting to learn Perl, even though it is a bit out-dated now.

EDIT: ⬆ This Tisdall book suggestion is really bad advice, so I crossed it out. It was great when it was first released into a world with no BioPerl, but everything in this book teaches the old, bad ways of doing things. It is so common that is worth mentioning that and leaving a note in place. Instead, take a look at the Modern Perl book, Beginning Perl by Curtis Poe, or Learning Perl by brian d foy.

Note that the Unix and Perl reference mentioned above is now a published book. There is a book website with more details on obtaining the print version.

ADD COMMENTlink modified 4.0 years ago • written 8.0 years ago by SES8.3k
3
gravatar for Tom Walsh
8.0 years ago by
Tom Walsh550
United Kingdom
Tom Walsh550 wrote:

Teach Yourself Perl in 21 Days and Beginning Perl are now more than 10 years old and Perl has changed a great deal since they were published.

I would recommend these books as good introductions to Perl as it is now:

Learning Perl 6th edition

Modern Perl

There is also a new edition of Programming Perl (the O'Reilly Camel book) just out.

ADD COMMENTlink written 8.0 years ago by Tom Walsh550

I agree Tom but I think Perl 6 will probably not be widely adopted.

ADD REPLYlink written 8.0 years ago by Gjain5.4k

Both of these books are about recent versions of Perl 5, not Perl 6.

I cannot see Perl 6 being widely adopted either. People who are tired of Perl 5 will move to Ruby or Python.

ADD REPLYlink written 8.0 years ago by Tom Walsh550
3
gravatar for Obi Griffith
8.0 years ago by
Obi Griffith18k
Washington University, St Louis, USA
Obi Griffith18k wrote:

Martin Krzywinski offers a really good 'Bioinformatics Perl Workshop' and he posts all his materials online. He covers too many topics to list here but his intro to perl includes scalar variables, text manipulation and regular expressions, lists, arrays, context, hashes, sorting, file I/O, subroutines, special variables, and string manipulation. Other courses include more intermediate perl topics, effective use of map, sort and grep in Perl, introductions to Unix, data mining and analysis at the command line, prompt tools, introductions to CGI and mod_perl, and more.

His website is a little confusing to navigate at first but once you figure it out, its a very rich resource for tutorials, tips and sample code.

ADD COMMENTlink written 8.0 years ago by Obi Griffith18k
2
gravatar for Gjain
8.0 years ago by
Gjain5.4k
Munich, Germany
Gjain5.4k wrote:

Hi Ram,

There are many resources you can look at:

I hope this helps.

ADD COMMENTlink modified 5 months ago by RamRS25k • written 8.0 years ago by Gjain5.4k

Both of these books are now more than 10 years old and Perl has changed a great deal since they were published. I would recommend these books as good introductions to Perl as it is now:

Learning Perl (6th edition)

Modern Perl.

There is also a new edition of Programming Perl (the O'Reilly Camel book) just out.

Modern Perl by chromatic

ADD REPLYlink written 8.0 years ago by Tom Walsh550
1
gravatar for andrew
5.1 years ago by
andrew20
United Kingdom
andrew20 wrote:

Self promotion here, but I'd certainly like bioinformatics experts to let me know how they find my Perl courses (especially Perl Essentials) https://geekuni.com/  Let me know if it needs more in the way of regular expressions - any good examples to work off would be a bonus!

ADD COMMENTlink written 5.1 years ago by andrew20
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