[Bioperl-l] Newbie question regarding the BioPerl Archive

[Jason Stajich]

> searchable interface to the mail archives.  Back when I was first getting
> acquainted with bioperl I used to search the archives "manually" looking
> for tips on how to use the Blast-parsing modules, especially.
>

Will have the web team look into the best way to search - another list
member posted the google query that would achieve this.
+bioperl +pipermail +SpecificQueryForBioperl

> Another thing I would like to see is an object hierarchy diagram
> showing which methods are inherited by whom, from whom.  Putting a
> little simple ascii text into each object's "pod" documentation
> detailing object lineage would be fantastic.  Something like:
>
>     Foo::Bar::ObjectName
>             V
>       Bio::Root::RootI
>
> would be great.
>
> I love that Perl lets you inherit multiple methods from multiple parent
> classes, but sometimes it can get a little confusing.  A bit of
> documentation would make this feature easier to use for "newbies" not yet
> used to OOP.  They may not even be aware of the parent class methods
> they could use.
>

We (at least I do) try and cut and paste the method docs from the
inheriting classes and list where the methods came from.  We are also
experimenting with some better POD2HTML translators that bring in the
inherited methods - see http://docs.bioperl.org.  The software that
generates this is still being developed so there are some bugs that
prevent this from being our production docs.

We'll see what other options are out there.

> Yours,
>
> Ann
>
> ---
>
> Ann E. Loraine
> http://www.loraine.net
>
> On Sun, 23 Dec 2001, Ewan Birney wrote:
>
> > 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?
> >
> >
> > (PS - have you tried Peter Schattner's tutorial? Did you like it? Can be
> > improved? If so --- how?)
> >
> >
> >
> > 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 ;).
> >
> >
> > > 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...
> >
> >
> > > 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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
>
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>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu