Bioperl Proposal for Perl5 Objects for Sequences, Alignments, and Phylogenies.

Mon, May 27 1996. The "current state" of the discussion. Development code is now available, and a small list of Java problems from the "Perl perspective".

Thu, 29 Feb 1996. The "current state" of the discussion. I realize that there are very few people who are knowledgable about Perl, Object Oriented Programming / Design, _and_ Molecular Biology, so you don't need to be a guru to send us feedback !!
You just need to read 3 files:

• 1. The above "current state" files (all you need to know about the Bio::Asn1_Seq object mentioned there is that it is "a Bio::Seq that includes many more instance variables (records), and offers much more functionality")

• 2. The following parts of the "Slightly modified proposal":
  • Revisions yet to be incorporated.
  • 1. Summary.
  • 2. Design Rationales.
    The 'empty sub-class' test dilemma is discussed in section 2.2 of the proposal.
  • 3.1. Sequences.
    (You can ignore 'numbers', 'names', 'desc', 'rels').
  • 3.2. Alignments.
    The most important part from my personal point of view.
  • 3.4. Phylogenies: "Ingroups", Trees, and Split Decomposition networks.
    I'm very eager to receive feedback here, too !
  • 3.5. Miscellanous Data.

Sun, 26 Feb 1996. Now feedback to the proposal is archived at the mailing list's archive, save the response by Peter Murray-Rust which was scrambled by the WWW-Archive software.

Mon, 5 Feb 1996. Posted the original version to the Bioperl Development List.

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Georg Fuellen