Naming the modules; Mailing lists

Georg Fuellen fuellen@dali.Mathematik.Uni-Bielefeld.DE
Tue, 25 Feb 1997 13:29:02 +0000 (GMT)

Steve wrote, -re- the draft announcement for the beta release,

> > [ 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?

A table of contents at the top is a VERY GOOD idea !

> 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

I'd rather not like to do this; adding a TOC should suffice ?! The main reason 
is that updating becomes more messy if there are a lot of pages; and I could
no longer just overwrite one page via netscape whenever you desire an update.
Also, a lot of ppl love longer pages b/c they can print them out in one go.
ok? If no, will change this asap.

> 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
                    USING and DEVELOPING ...
I feel that we need a list for user's questions, and there are not enough ppl
yet to mandate a split users<->developers. (Since the interaction users<->
developers is very useful, especially in the early stages, a split should 
only be done if too much mail is created.)
If you feel there should be a split, we should have vsns-bcd-perl for users,
and vsns-bcd-perl-guts for the developers.

I agree w/ all the other text.

>     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!

Correct; I'll beautify the final version !
> *** 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

As it happens, all stuff is automatically mirrored in USA and Italy,
as part of the VSNS-BCD mirroring system. However, in USA, index.html
is the default for the welcome page, and since there's no such file, will yield a directory
listing, so I always include the welcome.html to avoid confusion ! 
Therefore, the Q. is: do you feel an advantage if we ever mention these 
mirrors ? If no - let's drop the welcome.html.

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

heh, the last name appears in the next line..?:) Will rethink my .sig :-)

> > 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.

It helps; Techfak support has been very quick in deleting accounts in the
past, although I hope I can keep it rather long since I really need it;
OTOH, Techfak should be mentioned b/c I'm formally not in the maths department.

> >
> > 
> -------------
> > ===========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
> 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 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.  

Ok, although I'd love to see VSNSBCD mentioned... But life is a compromise :)

> ---
> 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'll add a TOC next. I'll also change the background.

> I would split the page into many sub-pages and make it much more
> user-friendly.

See above.

> 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). 

Your points are well-taken; will strip some sentences, too.

> ---
> 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

Will try my best keeping track of open issues !

> files, I will test them myself and then upload them to CPAN.

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.
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.

> Steve

Steve wrote, -re- my comments about his snail-mail
> > 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).

uh, uh... Have you got a solution for this?
Is it just DOS, or WinNT/Win95 as well ?

> > *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).

I hope that this can easily be worked in by adding a record 
{'numbering'}[$seq_number], once numbering is resolved for Bio::Seq. (It 
would need proper accessors, like {'names'}{'seqs'}[$seq_number]{'id'} and 
...{'desc'} do.)

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

best wishes,