Naming the modules; Mailing lists

Steven E. Brenner
Tue, 25 Feb 1997 13:42:16 +0900 ()

> Just got your snail, thanks !! I'll fax you a few pages w/ comments 
> probably tomorrow (using the on the envelope)

The fax number for me is +81 298 54 6041

> Just 4 comments now:
> *Pls reload Bio::UnivAln, take another look at consensus() !
Will try to do soon.

> *Also, the Fasta Regexp: I'm still not sure that mine is wrong !
Yours is ok; just strange.  Also, how does all of this code deal with
DOS-formatted files (i.e., that end in \r\n).

> *Re the last page of the snail: I still think it's easy to extract a column 
> as a string, but I guess it's the last time I'm mentioning that..
It is not easy to exract a column which corresponds to a desired column in
one of the sequences.  I _always_ index off of one of the sequences, not
the alignment (whose numbering is arbitrary and would change if a longer
sequence were added).

> *Re Overlap w/ Bio::Seq: Let's have Bio::Utils ? - But not right now...
That's fine.

> [ The following DRAFT should be reformatted+edited to reflect any new 
> version of Bio::Seq/Bio::UnivAln; the announcement is just a re-shuffling
> of the homepage. I HOPE I CAN SEND IT NEXT MONDAY at the latest; Chris ??? ]
> ========DRAFT bioperl@mole Farewell message==========

> Subject: Bioperl Beta Announcement; Mailing list moved !

The content of the message looks good, but its sheer bulk makes it a bit
overwhelming.  I think that better formatting and layout could help.  How
about a table of contents at the top?

Similar comments apply to the text of the bioperl web page.  I would
suggest making the page 1/10th of its current length, and putting all the
details onto sub-pages; details below

Contents of this Message:

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

> Dear subscriber to,
> 1) Bio::Seq (Sequences) and Bio::UnivAln (Alignments) are now in beta-status,
> see the announcement below. If you use the code, please mail us feedback !
Change to:

1.  The bioperl modules for sequences and alignments (Bio::Set) and 
    (Bio::UnivAln) have now been released for beta testing.  They have
    just been uploaded to CPAN sites.

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 acutally 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 bags and
>            alignments). 
>                Status: beta code, Version 1.002 from 21
>                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,

 ^^^^^^^ format all of this to use more columns.  Right now it is too
long.  Also, exdent the first line of each topic -- paragraphs are very
difficult to identify!

*** Delete all of the text from here until until my next comment
>            Manipulation of Phylogenetic data, and more
>            graphics/www stuff is in the pipeline.
>            For all modules, you will need Perl 5.002
>            installed. 
>         There's a developer's list
>, to which you
>         can subscribe by sending email to
>, with no subject
>         line, and the following message body: subscribe
>         vsns-bcd-perl
>         Significant updates will be announced on the list
>         vsns-bcd-perl-announce, to which you can subscribe
>         by sending email to
>, with no subject
>         line, and the following message body: subscribe
>         vsns-bcd-perl-announce
>         About the project.
>         We develop free software, in particular for handling
>         biosequence and alignment data. Perl is an excellent
>         "Glue Language" for interfacing C/Fortran code,
>         WWW/CGI, graphics (e.g. using PGPERL), numerical
>         analysis (e.g. using the Perl Data Language),
>         Java-based GUIs (just dreaming :-), and much more.
>         With the current development of a true Perl Compiler,
>         it is a serious competitor to C: it's got high-level
>         features, and relieves you from manual memory
>         management, segmentation faults, bus errors, most
>         portability problems, etc, etc. So much for the
>         prospects :-) 
>         About us.
>         We are loosely associated with the award-winning
>         VSNS-BCD BioComputing Courses; some students of
>         the 1996 course (Chris Dagdigian, Richard Resnick,
>         Lew Gramer, and others) have contributed code and
>         commentary, and the project is co-coordinated by
>         Georg Fuellen, one of the VSNS-BCD organizers.
>         Steven Brenner acts as the chief coordinator; he's
>         currently on travel but will be back online soon. 
**** Delete through here

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 hompage:

Note: Do NOT include the welcome.html

> best wishes,
>   georg
^^^^ give your last name here; most people don't know hwo georg is!

> fuellen@dali.Mathematik.Uni-Bielefeld.DE, fuellen@Techfak.Uni-Bielefeld.DE
^^^^ there's no reason to give two addresses -- it doesn't help anything.
Just give one.


> ===========Welcome message vsns-bcd-perl-announce============
> Welcome !
> For more information, please take a look at

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

Then tell people where to go for more informaiton.. the bioperl homepage
and the archives.

> A hypermail archive of this list is available at
> best wishes,
>   georg
>   http://www.TechFak.Uni-Bielefeld.DE/techfak/persons/fuellen/georgF.html

> ============Module list entry======================
> Bio::
> ::Seq            bmpO  Handle molecular sequences (DNA,RNA,protein) VSNSBCD
> ::UnivAln        bmpO  Handle alignments of molecular sequences     VSNSBCD
>   VSNSBCD  The Bioperl Project mailing list
>            Mail to with body
>            "subscribe vsns-bcd-perl". There is an announcement-only
>            low-volume mailing list too, mail with body
>            "subscribe vsns-bcd-perl-announce" instead.

Looks good, except, I'm going to change the VSNSBCD to just Bioperl.  


Regarding the homepage.  Right now it is long and cluttered -- and I find
that the color scheme makes things hard to read (but is kind of neat).

I would split the page into many sub-pages and make it much more

There should probably be separate subpages for

 1. Introduction
 2. Current modules
 3. Mailing list
 4. Related sites
 5. Contributors and sponsor

Right now, I find the text to be much to casual.  Well intentioned, but
difficult to read quickly.  I would strip out all the smileys and all of
the comments which require smilies.  In general, there should be fewer
sentences (which won't be read anyway) and more headers and outline bullet
points (which help people find what they're looking for). 


Please let me know once all of my comments on the snail-mails have been
considered and either implemented or rejected.  Once there are bundled tar
files, I will test them myself and then upload them to CPAN.