[Bioperl-l] Newbie question regarding the BioPerl Archive

[Elizabeth Bowen]

> From: Ewan Birney <birney@ebi.ac.uk>
> To: Elizabeth Bowen <ebowen99@ivillage.com>
> cc: bioperl-l@bioperl.org
> Subject: Re: [Bioperl-l] Newbie question regarding the BioPerl Archive
> 
> On 21 Dec 2001, Elizabeth Bowen wrote:
> 
> > It sounds like the developers already have their hands full for a
> > while.  (Understatement?!?) But when things settle down a little, can
> > I hedge a newbie suggestion?  (This may be something that could help
> > out all of the potential newbie BioPerl people from the O'Reilly
> > conference as well.)
> > 
> 
> We've got alot of time here for Newbies, and in particular I am aware that
> bioperl is not really newbie friendly - most of the developers in Bioperl
> use it for reasonably large scale genome/bioinformatics processing and our
> bias is for clean objects that we can extend easily - not for easy to
> learn objects.
> 
> 
> Nat (from Oreilly - I am not going to attempt to spell his last name as I
> know I will get it wrong!) suggested a "newbie friendly" Bio::Perl module
> that would give easier to learn access to the main objects --- do you
> think that would be a help?


Would I ever!!!!  That would be fantastic!

Hee hee hee!  You should have SEEN my face the first time I tried to work with BioPerl!  *grin*  I had already studied regular, non-OO Perl for about three months.  I had also read the O'Reilly books "Learning Perl," "Developing Bioinformatics Computer Skills" and "Beginning Perl for Bioinformatics."  At that point, I felt really prepared to start on BioPerl.  But then... I realized very quickly that I knew next to nothing about using OO Perl, which is integral to be able to work with BioPerl.  I spent the next week studying OO Perl for (no joke!) ten hours each day, and I still feel as though I have barely scratched the surface.  Its slowly starting to make sense, but a newbie module would definitely be helpful at this point!



> (PS - have you tried Peter Schattner's tutorial? Did you like it? Can be
> improved? If so --- how?)


Yes, I have tried Peter Schattner's tutorial.  I do have to admit, though, that I found doing the Pasteur BioPerl tutorial first was very helpful in assisting me through the tutorial in the BioPerl documentation.  Schattner's tutorial is more like a guidebook rather than a hands-on tutorial, like the one from Pasteur, so it was better to do his second.

By the way, I would like to thank the person(s) who translated the Pasteur BioPerl tutorial from the bottom of my heart!  Bravo!


> In any case, don't fear about speaking up if you don't get something --
> we'll only get annoyed if you don't listen ;).


Oh, don't worry about that!  I definitely will be listening.  I just might not always understand what you are saying!  ;-)


> > I was delighted to find out that there was a Bioperl archive page:  
> > http://bio.perl.org/pipermail/bioperl-l/
> > 
> > Is there some way to search for a topic in the archive without having
> > to download it in its entirety or read through subjects for each month
> > of the archive?  I don't have enough space to download it and it is a
> > chore to go through each month searching for a needle in a haystack.
> > 
> > Also, is there an FAQ page for Bioperl?
> > 
> 
> No-one has really had the energy to maintain one (we could maintain one
> through the Wiki right guys? Or we had a FAQ-o-Matic?). Elizabeth - if you
> would want to compile your top ten questions to start (or restart) a FAQ
> and then looked after it, then that would be great...


I'll do my best.  Right now, I'm just struggling to keep up.  Any other newbies who might be also wish to help with this effort would be welcome!


> > Sorry to add more to your plate.  I just would just like to be able to
> > solve a lot of my problems due to inexperience with Bioperl without
> > taking up anyone's time on the list.  I'll bet a lot of other newbies
> > feel somewhat self-conscious about that too.
> > 
> 
> I don't we mind - it usually takes us seconds to respond and saves you
> alot of pain - post away!
> 
> 
> 
> ewan

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