[BiO BB] (no subject)

Val Bykoski valb at vtek.com
Sat Sep 15 21:41:34 EDT 2001

Hi Indraneel,
    Thanx for your comments.
    I refer to the cell as a biological cell, and my point,
    to put it a little differently, was that data has to work
    inside a (realistic) cell model, not to sit passively in databases.
    Data grouping, visualization, etc. is better than nothing,
    but still there is a huge gap between data (nicely grouped, 
    visualized, etc) and their biological significance or context.
    I guess my point is that if you integrate data into a realistic 
    cell model, the model is both a predictive framework and 
    a (bio)context-sensitive database for the data.  Then,
    data is hidden and work inside the model for predictions,
    and does not require grouping, visualization, etc.
    Sure, the "realistic cell model" is a hard nut...but may be
    worth of efforts, in particular, for a data-driven model.
cheers, val
val at vtek.com

----- Original Message ----- 
From: "Indraneel Majumdar" <indraneel at indialine.org>
To: <bio_bulletin_board at bioinformatics.org>
Sent: Saturday, September 15, 2001 6:35 PM
Subject: Re: [BiO BB] (no subject)

> Hi,
> I'm sorry I didn't understand properly. Do you refer to the cell as a
> biological cell, or as a unit of useful data?
> In case of the former probably that's what we are trying to find out,
> together with the broader perspective of all cells working together.
> In case of the latter, we probably already have the units of data,
> sometimes related and sometimes not. Now is the time to seggregate them
> to it's smallest units and link them up using relations (yes, I'm
> implying relational database systems). We do however need to know what
> to expect out of this database, and also account for the fact that we
> can never know how to scale it when new types of data come along (but
> then this applies to every field). From my personal work, I have found
> that simply being able to group and ungroup data shows up hidden facts,
> and also generates ideas for new studies. (If you're curious, I use
> PostgreSQL :)
> \Indraneel
> On Thu, Sep 13, 2001 at 10:34:18PM -0400, Val Bykoski wrote:
> > Mike,
> > To me, data integration is part of more serious problem 
> > how to build a realistic cell model.  Without cell model,
> > there is no (computational) framework to integrate the
> > data around.  Data needs to be integrated into smth biologically
> > significant - otherwise the data is very much useless...
> > my best, val
> -- 
> http://www.indialine.org/indraneel/
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