[BiO BB] software categories

Val Bykoski valb at vtek.com
Wed Apr 25 20:46:11 EDT 2001

A couple of points, Jeff:
    Within the complexity of the categorization task itself,
    your suggested categorization seems to me pretty good.

    My point with biocontext and biofunction is to
    _add_ (when useful) the description of the environment 
    in which the object exists/expresses itself ("in vivo", 
    "in vitro", or smth like that but more specifics) 
    and of the biological function  the object implements 
    or is part of the implementation

    1. Biocontext: any (macro)molecule operates in
    an environment which needs to be included in the description.

    2. Biofunction: any (macro)molecule (being in an env)
    implements some biol function (or is a part of the implementation,

    And the whole idea here is that in bioinformatics the methods 
    and tools need to be integrated (as much as possible) into biol 
    "reality" which in many cases can be represented in terms of 
    "structure-function" relationships.  A structure w/out the function
    involved is very much a lost knowledge..

    Unfortunately, this sounds too general. i'll give it another try 
    in awhile.

cheers, val

----- Original Message ----- 
From: "J.W. Bizzaro" <jeff at bioinformatics.org>
To: <bio_bulletin_board at bioinformatics.org>
Sent: Wednesday, April 25, 2001 12:20 PM
Subject: Re: [BiO BB] software categories

> Val Bykoski wrote:
> > 
> >     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).
> That's a good point.  I hadn't considered these.  But where should they go? 
> They could be alternatives to "manifestation", e.g.
>     [OBJECT]
>     Amino Acid/Protein
>       Kinase Activity
>         Simulation
> They could be in addition to manifestation:
>     [OBJECT]
>         [BIOFUNCTION]
>           [PROGRAM FUNCTION]
>     Amino Acid/Protein
>       Tertiary Structure
>         Kinase Activity
>           Simulation
> Or they could be in program function:
>     [OBJECT]
>     Amino Acid/Protein
>       Tertiary Structure
>         Functional Analysis
> Also, could you give me an example of "biocontext"?
> 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
> --
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