[Biodevelopers] RFC: software categorization schemes and foundries

[J.W. Bizzaro]

Greetings.

Matt Cowan just reminded me that we lack a good software categorization scheme
at Bioinformatics.Org, what could even lead to foundries.

I've had some ideas about how to categorize bioinformatics software.  It's an
interesting problem, being you can categorize several aspects of such
software: biological subdiscipline (e.g., crystallography), biological object
or taxon (e.g., a protein), manifestation (e.g., structure) as well as program
function.

I came up with some ideas about a year ago for the latter 3, and I managed to
dig them up and paste them below.  We'd appreciate some comments on how this
can be done, in general and specifically, even expanding into categories for
bioinformatics research and education.

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

The hierarchy is

    [OBJECT]
        [MANIFESTATION]
            [PROGRAM FUNCTION]

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


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...

A hypothetical AA sequence alignment program
-------------------------------------------
  Amino Acid/Protein
      Primary Structure (sequence)
          Comparing


Cheers.
Jeff
-- 
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
--