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
- Low volume moderated list, providing announcements of major
bioperl releases and upgrades
- Join by sending a message with ... to ...
- Web archive at http://....
- 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
While it may be a pain, it is entirely crucial if we are to retain
compatibility with the rest of the Perl community!
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 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:
> 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,
> 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:
Chop off the welcome.html, as discussed above