Back (for now)

Steven E. Brenner
Fri, 27 Jun 1997 13:55:06 +0900 (JST)

Hi Folks.

  Georg: Thanks for the quick, useful reply!

On Thu, 26 Jun 1997, Georg Fuellen wrote:

>   [ Note, I'm on vacation July 5 -> approx July 25. ]

Ok -- that corresponds with most of the time I'm away.

> >   Congratulations on the great job with the OiB electronic poster.  I
> > think you guys did a great job of putting that together.
> thanks -- SteveC and Chris deserve most of the credit !! 
> How about basing a Perl Journal article on it ??

Great idea! How should we arrange this?  Maybe SteveC and I could
coordinate this once I get to Stanford, with more input from you guys?  I
contacted Jon Orwant some time ago, and he indicated a willingness to have
a bioperl article at pretty much any time.  I think this should be
published after the CPAN release. 

> My interest will probably remain limited to sequences, at most I expect to deal
> w/ RNA structures in my PhD thesis work, and I'm not sure generic code 
> concerned w/ both RNA _and_ protein structures is a useful thing to have, or? 
> I'm mentioning this b/c as soon as you guys start working on modules for
> structures, you may shortly consider RNA structures, too, and maybe find
> out that I'm too pessimistic ?!

I think that the protein 3D structure module might reasonably include RNA
(and DNA)  tertiary structures.  However, I think RNA secondary structure
is very different from protein 3D or secondary structure.  Moreover, I
don't see any real advantage of conflating RNA secondary structure with

> > 3)  Releasing these darn things finally!!
> > 
> > Background info: the bioperl list at mole is now gone; the sysadmin
> > removed it because of junk mail it was attracting. 
> Not so nice. Given this, what's the best way to avoid manual subscription 
> of the bioperl@mole subscribers to our vsns-bcd-perl-announce list ??

Um, in your announcement message, you said that everyone had already been
put on vsns-bcd-perl-accounce and just gave instructions for removal.  So,
I don't see any change here.  I'm confused by the problems you suggest.

> I won't start reworking the announcement texts until the code is submitted
> to CPAN -- that was a (small) waste of time doing it in Mar/Apr, I should 
> have known better ;-) 


> I suggest that as soon as you're at Stanford, you bundle things together,
> incl. makefiles. Maybe SteveC will help, etc. Just today I realized that
> I'll probably soon need to replace some functions by C code, so I'd be happy
> if the make process would be designed w/ this in mind - if that's possible 
> at all. 

I am tentatively happy with this, but am concerned that it could be a
major delay. I am just at Stanford for 1 month before I disappear again
(for a few weeks), and during that time I'm attending two conferences and
need to make up my presentations for both of them!  Plus, I need to get a
new apartment, move in.  

I would not recommend using any C code at this point, as it is likely to
delay things further (though making the module designed to permit it at
the future is good idea). 

It would be best if, for example, UnivAln and PreSeq could be set up so as
to build out-of-the-box.  If this means removing some features, I think
that is better than requiring manual editing.  (You could require manual
editing to reinstate teh features.)  Then, if you can get those to me by
August 1, I promise to make a major effort to get the items on CPAN as
quickly as possible once I get to Stanford.

> > 4)  A bioperl meeting
> First of all, let's hear Chris on the issue -- any news on G.I.'s side ?
> Perl for G.I.'s "2nd generation" code ?? - would be great !!
> I cannot travel to the US without the additional justification of an
> International bioinformatics conference where I can present my PhD research
> stuff -- I've heard that there's gonna be another OiB meeting next year 
> in the US, coupled w/ ISMB 1998, it may be good to meet berore/during/after.

When/Where is ISMB 1998?  I have been scouring the web for this, without
any luck whatsoever. 

> Other outstanding issues on my list:
> Link to WWW-talk/poster from homepage (SteveC: is that ok, or did you do 
> last-minute changes that are not yet on the WWW ?)

Ok with me.

> My big prob with Bio::PreSeq/Bio::Parse is correctness: how do you verify 
> it's doing every conversion ok? test suite? regression w/ ReadSeq?

I assume that it at least works most of the time!  Unless we're confident
that this works perfectly, why don't we list it as a 'use at your own
risk'.  We should make up a test suite, but I think that is unecessary for
the release of 'PreSeq'

> Should we have clone() or copy() for the function
> that returns a clone/copy of the object ?
> Maybe one is non-recursive (shallow), but the other is ``deep''?!

I liked your (Georg's) idea:  clone() is deep, copy() is shallow.  

> (Which lab? I know quite some ppl there..)

I'll be at the Bioinformatics Center, National University of Singapore...

Best regards,