Naming the modules; Mailing lists
Wed, 26 Feb 1997 11:08:58 +0000 (GMT)
> 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?
> 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 http://scop.mrc-lmb.cam.ac.uk/pub/bioperl/)
> > >
> > > 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 (Better a short welcome message than an outdated one.)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 A couple of sentences should be chosen which won't go out of date.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
If you have time to write a long welcome message, pls go ahead, and I'll set
> > First, we need to resolve the following
> > >>>>>>>>
> > [I wrote] [...]
> > http://world.std.com/~swmcd/steven/Perl/module_mechanics.html
> > 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 !
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 firstname.lastname@example.org,
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
email@example.com 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:
3. Information about Bio::Seq and Bio::UnivAln
<CUT AND PASTE FROM HOMEPAGE, BEAUTIFY FORMATTING IN FINAL POST :->
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: