[BiO BB] (no subject)
valb at vtek.com
Sat Sep 15 21:41:34 EDT 2001
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.
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)
> 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 :)
> 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
> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
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