[BiO BB] software categories

[J.W. Bizzaro]

I've extensively re-worked the categorization scheme.  I think that it is much
more flexible right now.  Please take a look and see if the applications that
you know will fit.  And please let me know if not.

Oh, and feel free to add anything that's missing.  THANKS!

Note: Words [IN CAPS WITH BRACKETS] are for organization and would not appear
in category description.

The hierarchy is

    [OBJECT]
        [MANIFESTATION]
            [PROGRAM FUNCTION]

Examples using some of my own programs:

"MeltSim" (http://bioinformatics.org/meltsim/)
----------------------------------------------
  Nucleotide/Nucleic Acid
        Secondary Structure
            Simulating
                Thermodynamics

"Piper" (http://bioinformatics.org/piper/)
------------------------------------------
  Generic/Multiple Objects
        Generic/Multiple Manifestations
            Peripheral to Programs
                Networking

Also...

AA Sequence Alignment
-------------------------------------
  Amino Acid/Protein
      Primary Structure (sequence)
          Comparing


Here goes:

-------------------------------

[OBJECT]

    [MOLECULE OR MACROMOLECULE]

        Nucleotide/Nucleic Acid
        Amino Acid/Protein
        Fatty Acid/Lipid
        Sugar/Polyaccharide
        Other Molecule    
        Generic/Multiple Molecules

    [BIOLOGICAL STRUCTURE]

        Tissue
        Organ
        System
        Organism
        Other Biological Structure
        Generic/Multiple Biological Structures

        Generic/Multiple Objects

-------------------------------

[MANIFESTATION]

    [MOLECULE OR MACROMOLECULE]

        Primary Structure (Sequence)
        Secondary Structure
        Teriary Structure
        Quaternary Structre
        Biosynthesis
        Expression
        Other Molecule Manifestation
        Generic/Multiple Molecule Manifestations

    [BIOLOGICAL STRUCTURE]

        Genotype
        Phenotype
        Development
        Life Cycle
        Other Biological Structure Manifestation
        Generic/Multiple Biological Structure Manifestations

        Generic/Multiple Manifestations

-------------------------------

[PROGRAM FUNCTION]

    Viewing
    Editing (Non-Annotating)
    Annotating
    Assembling
    Quantitating
    Comparing
    Simulating

        Kenetics
        Thermodynamics
        Other
        Generic/Multiple

    Genetics

        Punnett Square
        Pedigree
        Generic/Multiple

    Phylogenetics

        Parsimony
        Neighbor Joining
        Maximum Likelihood
        Tree Drawing
        Other
        Generic/Multiple

    Databases

        Comparing
        Querying
        Submitting
        Other
        Generic/Multiple

    Peripheral to Programs

        Networking
        Language Library
        Other
        Generic/Multiple

    Other Function
    Generic/Multiple Functions

---------------------------





-- 
J.W. Bizzaro                                jeff at bioinformatics.org
Director, Bioinformatics.org        http://bioinformatics.org/~jeff
"As we enjoy great advantages from the inventions of others, we
should be glad of an opportunity to serve others by any invention
of ours; and this we should do freely and generously."
                   -- Benjamin Franklin
--