Naming the modules; Mailing lists

[Georg Fuellen]

SteveBr wrote,
> I take it we agree on the text for the mailing-list annoucment?  Do you
> want to send the 'final beta' text to be checked?

see below!

Re: homepage..

> I suppose I could live with the long page, and the improvements made are
> already very significnat.  But let's keep open the possibility of multiple
> pages in the future?

ok

> Some comments:
> 
> - The texture-mapped DNA is kind of neat.  Unfortunately, unless you know
> that it is DNA, you would have difficulty recognizing it as such!  
> 
> - The headers should be put in bigger text
>
> - The related links should be closer together (get rid of the <p> marks
> 
> - The table of contents should be more detailed (e.g., include the 
> names of the two modules at the top)

done; check again..

> - The mailing list really should be on a separate page, because it needs
> to include the charter.  Also, right now the paragraph format of the
> information about the mailing lists is difficult to interpret.  More about
> lists below.

will wait for your charter; I believe time is better spent elsewhere,
but your opinion counts.

> - Why don't you use index.html as the default welcome page on your site?
> index.html is the standard default page!   I do think that the mirror is

Well, changing this would take a long time ! Just think of ``welcome.html''
as a friendly message: ``You're welcome to browse here''. Psychology, heh :-)

> potentially useful.
> 
> Regarding lists
...
> > > I would include a lot more informaiton here.  First, give a brief
> > > introduction to the bioperl projects (2 sentences).  The explain the list
> > > (2 sentences), and point people towards a charter (similar to the old one
> > > at http://scop.mrc-lmb.cam.ac.uk/pub/bioperl/)
> > > 
> > > Then tell people where to go for more informaiton.. the bioperl homepage
> > > and the archives.
> > 
> > Note that this means double work in updating; no time for that I think !
> > (Better a short welcome message than an outdated one.)
> > There should definitely be a pointer to a general mailing list charter 
> > (no spams, etc), if you prepare one.
> 
> A couple of sentences should be chosen which won't go out of date.  If you
> look at the old bioperl list charter, you can see that it is still mostly
> relevant.

If you have time to write a long welcome message, pls go ahead, and I'll set
it up.

> > First, we need to resolve the following
> > >>>>>>>> 
> > [I wrote] [...] 
> > http://world.std.com/~swmcd/steven/Perl/module_mechanics.html
> > also reflects that resentment, and the offerings -re-
> > ``Building Related Perl Modules'' and
> > ``Testing a module from a Perl program'' made me feel uneasy.
> 
> I don't understand why.  Note that there is also documentation about this
> stuff in the actual Perl manpages	

The pages's author isn't happy either; also it's too complicated.
I couldn't figure out how to administer more than one module in development..
I guess I'd need detailed instructions.. But I believe it would take 
you just 15 minutes to do the right setup ?!

> > But as the page's author says, ``You get used to it. Really.'' Oh well.
> > Maybe you've got better recommandations than the ones on that page ?
> > <<<<<<<<
> > As I said, I've run into trouble anyway, getting a variety of make problems.
> > I'll work again through the module_mechanics recommandations of _you_
> > recommand them. But maybe it's easier if you just do this yourself, because
> > then you can set things up in exactly the way you like. I can prepare
> > a Bio::UnivAln tar file _without_ the PGPLOT stuff as soon as you request it.
> 
> Yes -- please build it without any PGPLOT stuff for now, if that's what's
> causing the problem. 
> 
> 
> 
> Right now I'm running on a temporary computer system, so I do not have any
> decent facilities for doing much of anything.  (That's part of why I made
> my comments on the paper!)  If you can get me a fully working package, I
> can test it.

Go get Bio::UnivAln, now without the PGPLOT stuff, from the homepage !

best wishes,
georg

===========DRAFT=============
Subject: Bioperl Beta Announcement; Mailing list moved !

 1. Bio::Seq and Bio::UnivAln in public beta
 2. Bioperl mailing list moved
 3. Bio::Seq and Bio::UnivAln beta release announcement
 4. How to get more information

Dear subscriber to bioperl@mole.bio.cam.ac.uk,

1.  The bioperl modules for sequences and alignments (Bio::Seq and
    Bio::UnivAln) have now been released for beta testing.  They have
    just been uploaded to CPAN sites. You can also get them from
    http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/welcome.html

2.  The bioperl mailing list is being reorganized and the old
    bioperl@mole.bio.cam.ac.uk list is going away entirely.  Replacing it
    is the list 'vsns-bcd-perl-announce,' a moderated list with
    announcements about bioperl.  To be removed from the list, send this
    mail (including headers) to:
        fuellen@dali.mathematik.uni-bielefeld.de.

    In addition, the unmoderated list vsns-bcd-perl is for people
    interested in using and developing bioperl code.  You can join that
    list by sending mail to:
        majordomo@lists.uni-bielefeld.de
    with the body text:
        subscribe vsns-bcd-perl

3.  Information about Bio::Seq and Bio::UnivAln

<CUT AND PASTE FROM HOMEPAGE, BEAUTIFY FORMATTING IN FINAL POST :->
        Bio::Seq, a Perl module for reading, parsing, writing, slicing, and
        manipulating single biosequences. 
           Status: beta code, Version 0.020 from 12 Febr 97. 
           Special features: manipulate and parse biological sequences 
           In progress: Tight integration with ReadSeq program, robust
           formatting and output 
           Chief Developer ("Pumpkin Holder"): Chris Dagdigian,
           cdagdigian@genetics.com. 

        Bio::UnivAln, a Perl module for reading, parsing, writing, slicing, and
        manipulating multiple biosequences (sequence multisets and
        alignments). 
           Status: beta code, Version 1.003 from 25 Febr 97. 
           Very flexible slicing, mapping, consensus, (in)variable sites,
           gap-free sites, reverse, complement, and reverse complement. 
           Of special interest: You can specify functions for the slicing
           operation, e.g. use a function that returns true if column
           characters are "different" according to some definition of yours,
           and slice all the other columns off... Voila - you have the variable
           sites only ! 
           Also, you can apply a function to some columns and/or rows, and
           receive the list of function values. E.g. use a function that returns
           the majority residue based on your own criteria, apply it to the
           columns, and there you go: Your consensus sequence ! 
           Planned enhancements: More CGI/Graphics stuff (a CGI script is
           in alpha status); implement an option to use the Perl Data
           Language for the internal representation -> better performance,
           but you need C installed. 
           Also planned: ReadSeq for format handling, sequence alphabet
           checks, internal support for more formats e.g. Nexus. 
           Chief Developer ("Pumpkin Holder"): Georg Fuellen,
           fuellen@Techfak.Uni-Bielefeld.DE,
           fuellen@dali.mathematik.uni-bielefeld.de. 

        For all modules, you will need Perl 5.002 installed. 

4.  More information about the bioperl project (including the
    mailing list charter, details about the projects and its
    contributers, and -- of course -- the modules themselves)
    can be obtained from the bioperl homepage:

      http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/welcome.html