[BiO BB] software categories

[Val Bykoski]

Hi Jeff/All,
    Yes, that adds more content and looks more convincing to me.
    I'd suggest also to integrate into the
    description the "biocontext" and "biofunction" components
    (meaning the description of the object' context and its biol
    function, respectively).
cheers,
/val

----- Original Message -----
From: "J.W. Bizzaro" <jeff at bioinformatics.org>
To: <bio_bulletin_board at bioinformatics.org>
Sent: Wednesday, April 25, 2001 12:32 AM
Subject: Re: [BiO BB] software categories


> 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
> --
>
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