Naming the modules; Mailing lists

Georg Fuellen fuellen@dali.Mathematik.Uni-Bielefeld.DE
Wed, 26 Feb 1997 11:08:58 +0000 (GMT)

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?


> 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
> > > 
> > > 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 (Better a short welcome message than an outdated one.)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 A couple of sentences should be chosen which won't go out of date.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] [...] 
> >
> > 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,

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,

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

2.  The bioperl mailing list is being reorganized and the old 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:

    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:
    with the body text:
        subscribe vsns-bcd-perl

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

        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,

        Bio::UnivAln, a Perl module for reading, parsing, writing, slicing, and
        manipulating multiple biosequences (sequence multisets and
           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,

        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: