I am new to Bioinformatics field. I am doing some kind of Genomics work. So I am trying to learn Perl and Unix. Can anyone suggest me from where to initiate these? Some basic books or tutorial online or some other web pages? Thanks.
Congratulations, you have chosen the right language!
- Just learn Perl http://learn.perl.org/
- The Perlmonks have a large tutorial section.
- http://www.perl.org/learn.html - more links and tutorials (edit)
- perl comes with a lot of built in documentation mainly for slightly advanced users, run:
perldoc perl perldoc perlintro
for an overview.
- The O'Reilly Camel and esp. Lama books are quite good. Beginning Perl for Bioinformatics not recommended, doesn't cover BioPerl, and dated.
Also, after learning perl you will need to develop some BioPerl skills.
Have a look at the Unix & Perl Primer for Biologists.
The Lama book is good for Perl beginners - be sure to get the most recent (6th) edition.
Perl has changed a lot in recent years so I would avoid books that are more than a few years old. Modern Perl is a good introduction to current best practices and you can download a copy for free.
1) Identify problem you want to solve. Pick something simple, like manipulating a large text file.
2) Read books, solve it
3) Read some more, and solve it a new way.
Personally, I didn't find the O'Reilly bioinformatics books all that helpful. I started with Learning Perl.
Perl is a good place to start. I would recommend these two resources that are available:
Beginning Perl (Free Online Book)
Perl is a well-established programming language that has been developed through the time and effort of countless free software programmers into an immensely powerful tool that can be used on pratically every operating system in the world. Perl started out as the "Swiss army knife" of computer languages and was used primarily by system administrators, but over time it's grown into an immensely robust language used by web-developers and programmers worldwide. It's also a great way to learn programming techniques and develop your own style of coding.
Beginning Perl for Bioinformatics is designed to get you quickly over the Perl language barrier by approaching programming as an important new laboratory skill, revealing Perl programs and techniques that are immediately useful in the lab.
I hope this helps.
Most of the biologists / non-programmers have difficulty in diving into this jargon and understanding concepts. I know quite a few of them who preferred working with examples. And they particularly found the book Perl by Example by Ellie Quigley very useful . It has staggering amount of examples and every concept is introduced as such. This should be a starting book if you are new to programming as well, I believe. It has some typos (or had in the earlier version), nevertheless, it should be an excellent starter.