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Help from the very start.

by vickie (Novice)
on Jun 14, 2005 at 23:38 UTC ( #466728=perlquestion: print w/replies, xml ) Need Help??
vickie has asked for the wisdom of the Perl Monks concerning the following question:

Hi there,

I'm brand spanking new here and could do with some help. Basically, I'm very interested in bioinformatics and will be doing a masters next year. However, knowing some basic Perl would be a great advantage. I've read up on the basic concepts but I want to try it out for myself. That's my problem. I have NO IDEA where to start. You'd think being a recent computer science graduate would leave me a little more clued up!

Anyway. I'm on Windows XP, and am asking for a little help on what to do...what should I download first, and all that jazz. I can't see the answer to this on the forum already, but if I've overlooked it, my apologies.

Thanks in advance,


Replies are listed 'Best First'.
Re: Help from the very start.
by merlyn (Sage) on Jun 14, 2005 at 23:47 UTC
Re: Help from the very start.
by BrowserUk (Pope) on Jun 14, 2005 at 23:46 UTC

    You can download the ActiveState binary distribution (5.8.7) here. That will get you started.

    A word of advice. When it asks you where to install it, choose c:\perl or similar in preference to c:\Program files\Perl. It's just easier in the long term.

    Oh. And welcome to the Monastery.

    Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
    Lingua non convalesco, consenesco et abolesco. -- Rule 1 has a caveat! -- Who broke the cabal?
    "Science is about questioning the status quo. Questioning authority".
    The "good enough" maybe good enough for the now, and perfection maybe unobtainable, but that should not preclude us from striving for perfection, when time, circumstance or desire allow.
Re: Help from the very start.
by GrandFather (Sage) on Jun 14, 2005 at 23:46 UTC

    Read through some of the Tutorial stuff in Tutorials and through some of the Categorized Questions and Answers stuff.

    Dip at random in to any of the Seekers of Perl Wisdom threads and look at the code that is offered in answers.

    Wander around the Monastery and peek into any of the rooms!

    Perl is Huffman encoded by design.
Re: Help from the very start.
by VSarkiss (Monsignor) on Jun 15, 2005 at 01:31 UTC
Re: Help from the very start.
by Qiang (Friar) on Jun 15, 2005 at 06:05 UTC
Re: Help from the very start.
by mdxi (Beadle) on Jun 15, 2005 at 06:01 UTC
    You'd think being a recent computer science graduate would leave me a little more clued up!

    No, I'd think it would leave you knowing how to do nothing but write Java programs on Windows. *rimshot*

    Snarkiness about the state of CS education aside, it's hard to go wrong with The Llama (Learning Perl) for getting started. Conway's OO Perl book is an excellent resource for getting a good solid grip on that side of things once you're ready. There's actually a book titled Beginning Perl for Bioinformatics, but I haven't read it (and I don't work in the field), so all I can say about it is that you might want to find a copy and scope it out.

    Once you get going, the contents of perldoc (especially perldoc -f) will likely become your primary reference source.

      Writing java programs? Schpiel and UML diagrams will often afford a pass.

      A recent Datastructures & Algorithms assignment seriously suggested it was ok to download an AVL Tree implementation because using other peoples code can be as difficult as implementing it yourself.

      I am accruing significant debt for a BEng in javadoc *rimshot*

      time was, I could move my arms like a bird and...
      No, I'd think it would leave you knowing how to do nothing but write Java programs on Windows.


      SLAM-DUNK!!! {sound of backboard shattering}
Re: Help from the very start.
by tphyahoo (Vicar) on Jun 15, 2005 at 07:50 UTC
    Learn regexes. That's why you want to learn perl right? All those chainsaws for munging your dna? That's why I wanted to learn perl, at least at first. (Then I saw other possibilities and there was *really* no turning back... but that's another story. :) )

    So, treat perl like the control panel behind the most powerful text manipulation toolset on earth. :)

    How to learn regexes? Start using them. Perl one liners. Perlretut, in the perl documentation. In my case, it helped also to have some pretty gui tools to learn this stuff. Regex coach is free, and awesome. Editpad is not too expensive, awesome for regex find and replace. Also comes with a very good intro to PCRE (perl compatible regular expressions) tutorial, included in the documentation, and free online. Emacs is free, awesome for regex find and replace, but not as user friendly as editpad in my opinion (so I still haven't really learned how to use it, though it's on the to do list).

    Make regexes your friends. The rest of perl will come naturally.

Re: Help from the very start.
by Anonymous Monk on Jun 15, 2005 at 11:28 UTC
    Hi, Being in bioinformatics myself, I can say that Perl is an excellent choice. To be very honest, I found the Perl Cookbook to be of real assistance, offering the answers 'as you go'. To me it seems learning is more easy that way, because you get the knowledge when you need it. Furthermore, look into the BioPerl project (, they have a great big deal of ready-made subroutines, supported by a great number of people around the world. As an aside, you might also want to dig into the R statistical language, available at There is a project called bioconductor ( also offering loads of packages for dealing with bioinformatics problems. Bioperl and R run on *NIX as well as windows platforms, although some things just run better on *NIX. Good luck! Henk van den Toorn
Re: Help from the very start.
by Cody Pendant (Prior) on Jun 15, 2005 at 06:08 UTC
    What is the canonical O'Reilly book, I'd like to ask other monks, for this person.

    I started with Learning Perl (actually I didn't but I'm blanking that Dummies book from my memory!), but that was because I knew nothing about programming.

    For someone who's a "recent computer science grad" (that does mean they know something about programming, right?) what's the suggested entry point?

    ($_='kkvvttuu bbooppuuiiffss qqffssmm iibbddllffss')
    =~y~b-v~a-z~s; print
Re: Help from the very start.
by geekgrrl (Pilgrim) on Jun 15, 2005 at 16:09 UTC
Re: Help from the very start.
by monkey_boy (Priest) on Jun 15, 2005 at 09:08 UTC
    Nothig to do with perl but ...
    install Linux, (or dual boot your XP box)

    This is not a Signature...
      Cheers everyone! Especially for those articles, I'll have a good read later.

      I downloaded the binary distribution, but now I'm stuck. I don't know what to open. I keep on thinking there should be a nice easy interface like BlueJ, so that I can edit and compile to my hearts delight, however I'm begining to get the feeling that it's not that simple.

      I shall carry on having a bash at it anyway. I'll keep y'all posted.


        Having gone through similar steps in not-so-distant past, I would advise a few things:

        1. Get a book on Perl. I have one from Sybase, but believe that O'Reily has the best one... And it is much easier to absorb information while reading it from the book comparing to computer screen (at least, that's how it is for me and quite a few people I know)

        2. I believe you already installed ActivePerl on your XP box... Get a nice editor, preferably free, with syntax coloring etc... whatever you will be comfortable working with. Try a few at first, then choose... For example, I liked PSPad

        3. Try scripting, but choose good purposes for them. I mean, work on something that's at least somewhat important for you so that a working script will boost your self-confidence and make you feel you've accomplished something.

        4. As you progress on the Perl path, try to make your code {smaller|more readable|obfuscated} in several different ways - it's a great learning way and fun too...

        5. Keep visiting here as often as you can - that's the place for the most of good advices and information!


        Good luck!

        An idea is not responsible for the people who believe in it...

        I recommend the editor gvim - it's free and has very good context-highlighting for perl (and just about everything else). Create a text file called, and put your code in it. If you edit in one window and run with a command line 'perl' in another window, it should be fine. There's no compilation step with perl, so you don't have to worry about that one.

        ActiveState also do a rather nice IDE, but its fairly expensive and needs a reasonably chunky computer.

        If I found myself having to write Perl on a Windows system I would probably set course for Cygwin to get myself a decent shell (bash), although it is possible to get the job done with cmd (the shell that comes with Windows XP). Then I'd get myself a decent text editor. I'm pretty sure that Emacs is available through Cygwin, but Emacs is quite scary for a newbie. JEdit might be a good choice, it has many of the benefits of Emacs, but without the need to know weird key combinations.

        Oh, and ActiveState have some documentation for getting started with Perl on Windows.

        There are a few Perl IDE's around - eh voila

        I used Perl Scripting Tool when I was first learning, but that appears to be dead. Perl Builder looks quite interesting...

        time was, I could move my arms like a bird and...

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