Naming the modules; Mailing lists

Steven E. Brenner
Thu, 27 Feb 1997 12:58:46 +0900 ()

The Web page looks great!  The improvements (though almost entirely in
style rather than content) are really dramatic and -- I think -- make it
much more usable.

A handful of new suggestions:

- "Tersify" the Bio::UnivAln description.  Right now there are a lot
of long sentences and unnecessary exclamation points.  While I understand
and agree the intent (hey: this is really cool!), it is difficult to read.

- Provide a gzipped tar file for Bio::UnivAln.  The net is slow enough
without having to download uncompressed data

- The mailing list info is much better.  However, I would recommend
bulletting that too, and listing the announce mailing list before the
development/discussion one.

  * vsns-bcd-perl-announce
     - Low volume moderated list, providing announcements of major
       bioperl releases and upgrades
     - Join by sending a message with ... to ...
     - Web archive at http://....

  * vsns-bcd-perl
     - Unmoderated list for development and discussion of bioperl
       modules.  Potentially high volume.
     - Join by sending a message with ... to ...
     - Web archive at http://...

> > - 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.

I'm quite busy right now finishing a very late review.  So, I can't do
this right now.

It is absolutely essential, however, that the introductory message and the
charter list how to get off of the list!

Also, can you put an X-URL: header on the lists, pointing to the lists

> > - 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 :-)

Why would it take a long time?  Couldn't you just make a symbolic link
from index.html to welcome.html, as a simple hack to effect this?

I always thought the "welcome.html" was pretty dorky sounding!

> 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 ?!

If I had the right setup, I could probably do it in less than 15 minutes.
But as it stands, I can't do much at all.

While one page's author is unhappy about the module packaging procedure,
note that well over a hundred people have packaged their modules.  Indeed,
I don't know of any recent (within the past year) modules which are not
properly bundled.

While it may be a pain, it is entirely crucial if we are to retain
compatibility with the rest of the Perl community!

> ===========DRAFT=============
Looks great!
Once the code is 'shipped' to CPAN, this can be sent.  (Please make sure
to wait until it is indeed on CPAN.)

> 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
The main beautifying I would recommend is 
 1. Moving the text to have smaller margins
 2. Ex-denting (un-indenting) the first line of each bulleted point
    (Like Status, Special features, etc.)

>         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
>         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,
>         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:
Chop off the welcome.html, as discussed above