Naming the modules; Mailing lists

[Georg Fuellen]

Hi Steve,

> 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.

thanks!

> 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.

will modify this soon, though I believe ppl can just scan the page
for the information they want - I they're not interested, they'll move on.

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

will do this w/ the next release

> - 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.
                   ~~~~~~~~~~~~~~~~~~~~~~~~
This sounds very negative/un-inviting, how about
``Bioperl development issues will be moved to a seperate
           list if the volume becomes high.''

>      - Join by sending a message with ... to ...
>      - Web archive at http://...

All done. In general, though, I think we shouldn't spend more time on this,
improving WWW pages is a bottomless pit :-)

> > > - 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!

Majordomo automatically tells subscribers how to get off; those that we move
from your list to vsns-bcd-perl-announce get the advice to send email to me; I 
can append such an advice to each message sent via that list.

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

Majordomo can do this, but I need to find out how. Majordomo can also prefix
Subject lines w/ ``Bioperl:'', have an X-Unsubscribe, etc... 
This is another bottomless pit: So much that could be done and so little 
time :-/  (btw, the guy who maintains our majordomo is
working on a WWW-Interface to all this admin stuff.)

> > > - 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?

If we present stuff offline on our multimedia PC, every symbolic link
is one too much !

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

That is a matter of personal taste I guess..

> > 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!

Maybe I can find time over the weekend to retry this - but I need to make
one thing sure: Do you agree w/ the recommandations at
http://world.std.com/~swmcd/steven/Perl/module_mechanics.html ?
I cannot afford spending time on this and discovering later that it's
not the right way to do it.
[ ] agree [ ] don't agree, ______________________________________

> > ===========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.)

Yes, unless this causes a delay of more than a few days; then we need to 
rely on our own mirroring system to distribute the stuff. I think
it wouldn't do much harm to announce CPAN availability seperately 
a few days later.

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

I will, since you really really insist on this... :-)
But I believe we spend too much time on such details - it's just not worth it !
Think of it this way: If our code is good, ppl will use it
even if our presentation is just 95%-optimized !

best wishes,
georg

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